Complex genetic regulation of flowering time

May 26, 2020

Plant researchers from Kiel analyse the influence of genetic information on the onset of plant flowering using the example of thale cress

All flowering plants pass through a flowering period at the transition from the growth to the reproductive phase. Its beginning is determined by complex plant regulatory mechanisms. It also depends on environmental conditions, including temperature and day length. The determination of the start of flowering is an important lever with which plants can react to variable environmental conditions. A flowering plant adapts to drought or higher temperatures by, for example, bringing forward flowering under unfavourable conditions. In this way, it tries to start its reproductive phase earlier and still ensure that it can reproduce. A better understanding of the relationship between plant control and environmental influences is therefore important for assessing the susceptibility or resistance of different plants to climate change and the associated changes in agricultural cultivation conditions. Plant researchers around the world are therefore investigating the mechanisms involved in the control of flowering, including their genetic regulation.

Last year, a research team from the Botanical Institute at Kiel University demonstrated the involvement of the so-called POCO1 protein in the regulation of flowering time in a frequently studied plant model organism, the thale cress (Arabidopsis thaliana). In a follow-up paper recently published in the journal BMC Plant Biology, researchers from the Department of Botanical Genetics and Molecular Biology headed by Professor Frank Kempken analysed the genetic basis of these proteins, plant ribonucleic acid (RNA), using high-throughput sequencing methods. This enabled them to identify the genetic expression and variation of these proteins, which in Arabidopsis are associated with the regulation of flowering time.

Differences in the genetic repertoire
In order to investigate the so-called gene expression associated with flowering, the research team active at the Kiel Plant Center (KPC) at Kiel University carried out comparative analyses of plants at different stages of development - in each case in early flowering so-called poco1 plants and the unaltered wild types. The research team compared identical developmental stages in both variants and was able to identify significant differences: "The differences are particularly evident, for example, in a particular group of genes," emphasizes Hossein Emami, a research associate in Kempken's Kiel research group. "These include the so-called 'Flowering Locus T' (FT) gene, which is regulated very differently in poco1 and wild type plants," Emami continues. The upregulation of the FT gene is therefore probably directly related to an earlier flowering time of the thale cress.

In addition, the Kiel researchers investigated a second mechanism involved, which they had also discovered in the previous work. A number of genes in Arabidopsis seem to be related to a specific plant signalling pathway, which is usually downregulated in early flowering plants. These so-called ABA signals are responsible for the production of a flower-inhibiting plant hormone that needs to be deactivated at the transition from the growth to the reproduction phase. Gene expression analysis showed that the genes responsible for ABA signals were downregulated in early flowering plants compared to the wild type. "These signals therefore play another key role in controlling flowering time. Their inhibitory effect on the onset of plant reproduction can therefore be switched off under stress conditions, as the downregulated expression of the genes involved suggests," Emami continues.

Gene regulation contributes to early flowering
The Kiel research team was thus able to confirm the mechanisms of flowering time control by means of their global gene expression analysis. The up- and downregulation of certain genes therefore apparently also contributes to the fact that the POCO1 protein can additionally intervene in the ABA signalling pathway and thus trigger up to four days earlier flowering. As a consequence, further stress-related genes, in particular those associated with drought, appear in the early flowering plants, which can be seen, among other things, in the drought sensitivity of these plants.

"In summary, we have discovered that a certain genetic variant in Arabidopsis, which is responsible for an earlier flowering time, also leads to a number of other regulatory adaptations," said Kempken. "This includes, for example, the cellular mechanisms of flowering time control or the regulation of stomata to control water losses. Overall, this will help us to better understand the genetic characteristics that are expressed in early-flowering plants and that cause them to deviate from the wild type," Kempken continues. The KPC research team thus identified another important building block that will improve our understanding of plant flowering time regulation, especially under stress conditions, in the future. These findings could help plant breeding in the future to adjust the flowering time of important crops so that they can continue to grow even under drastically changed climatic conditions.

Energy of the future: photosynthetic hydrogen from bacteria

May 08, 2020

Kiel research team investigates how cyanobacteria can be transformed into hydrogen factories

The transition from fossil fuels to a renewable energy supply is one of the most important global challenges of the 21st century. In order to achieve the internationally-agreed target of limiting global warming to a maximum of 1.5 degrees, the international community must drastically reduce global CO2 emissions. Although Germany was long considered a pioneer in this energy transition, a wide-ranging switch to renewable energies in the energy sector still remains a future scenario here. In this regard, hydrogen could play an important role in the future as a promising, potentially climate-neutral energy source. Used in fuel cells, it provides energy for various applications, and only produces water as a waste product. At the moment, hydrogen is primarily obtained from the electrolysis of water - and this process initially requires energy input, which has so far mostly come from fossil fuels. A climate-neutral hydrogen economy, i.e. the use of so-called green hydrogen, requires that hydrogen production is based exclusively on renewable energy. Researchers are trying to exploit such a sustainable energy source, for example by means of photosynthesis. Ever since, photosynthesis has provided mankind with energy from sunlight, either in the form of food or as fossil fuels. In both cases, solar energy is initially stored in carbon compounds, such as sugar. If these carbon compounds are exploited, CO2 is liberated. Photosynthetic CO2 fixation is essentially reversed in order to recover the solar energy from the carbon compounds.

At Kiel University, associated to Professor Rüdiger Schulz, the junior research group ‚Bioenergetics in Photoautotrophs’ at the Botanical Institute, led by Dr Kirstin Gutekunst, investigates how this carbon cycle - and the resulting CO2 emissions - can be avoided during energy conservation. "For this purpose, the storage of solar energy directly in the form of hydrogen is particularly promising - this creates no CO2 and the efficiency is very high due to the direct conversion," says Gutekunst to explain her research approach. With her team, she investigates a specific cyanobacterium: via photosynthesis, it can produce solar hydrogen for a few minutes, which is however subsequently consumed completely by the cell. In their current study, the Kiel researchers describe how this mechanism could be used potentially for biotechnological applications in future: they were able to couple a specific enzyme of the living cyanobacteria, a so-called hydrogenase, with the photosynthesis in such a way that the bacterium produces solar hydrogen for long periods of time, and does not consume it. The scientists published their findings today in the renowned scientific journal Nature Energy.

Cyanobacteria as hydrogen factories
Just like all green plants, cyanobacteria are able to perform photosynthesis. During this process, solar energy is used to split water and to store the solar energy chemically - especially in form of sugar. Electrons pass through so-called photosystems in which they undergo a cascade of reactions that ultimately produce the universal energy carrier adenosine triphosphate (ATP) and so-called reducing equivalents (NADPH). ATP and NADPH are subsequently required for CO2 fixation to produce sugar. Thus, the electrons needed for the production of hydrogen are normally part of metabolic processes which provide the cyanobacteria with stored energy in the form of sugar. The Kiel research team has developed an approach to redirect these electrons and stimulate the metabolism of the living organisms to primarily produce hydrogen.

"The cyanobacterium we investigate uses an enzyme, a so-called hydrogenase, to produce the hydrogen from protons and electrons," says Gutekunst, who is also a member of the Kiel Plant Center (KPC) research network at Kiel University. "The electrons used in this process come from photosynthesis. We succeeded in fusing the hydrogenase with the so-called photosystem I in such a way that the electrons are primarily used for the production of hydrogen, while the normal metabolism continues to lesser extents," continues Gutekunst. In this way, the modified cyanobacterium produces significantly more solar hydrogen than in previous experiments.

Ability to repair itself
Similar approaches for hydrogen production by using fusions of hydrogenase and photosystem already existed in vitro, i.e. outside of living cells in test tubes, or on electrode surfaces in photovoltaic cells. However, the problem with these artificial approaches is that they are typically short-lived. The fusion of hydrogenase and photosystem must be laboriously re-created, again and again. In contrast, the path followed by the Kiel research team has the major advantage of potentially functioning indefinitely. "The metabolism of living cyanobacteria repairs and multiplies the fusion of hydrogenase and photosystem and passes it on to new cells during cell division, so that in principle, the process can continue permanently," emphasises project leader Gutekunst. "With our in vivo approach, we succeeded in producing solar hydrogen with a fusion of hydrogenase and photosystem in a living cell for the first time," she continues.

One of the current challenges is the fact that the hydrogenase is deactivated in the presence of oxygen. The 'normal' photosynthesis that continues in the living cells, during which oxygen is released by the splitting of water, thus inhibits the production of hydrogen. In order to remove the oxygen, or more specifically, to minimize the quantity released, the cyanobacteria for hydrogen production are currently partly switched to so-called anoxygenic photosynthesis. This is not based on water splitting. Therefore, the electrons for hydrogen production currently partly derive from water splitting and partly from other sources. But the long-term goal of the Kiel research teams is to only use electrons from water splitting for hydrogen production.

Concepts for the energy of the future
Overall, the new in vivo approach offers a promising new perspective for establishing photosynthetic water splitting as a means of production for climate-neutral, green hydrogen, and thus advancing the generation of sustainable energy. In the medium term, further research on the metabolic pathways of cyanobacteria in Gutekunst’s group is particularly focussed on further increasing the efficiency of solar hydrogen production. "The research results of our colleague are an excellent example of how fundamental research on plants and microorganisms can contribute to solving social challenges," emphasises KPC spokesperson Professor Eva Stukenbrock. "We are thus making an important contribution in Kiel towards developing a sustainable hydrogen economy as a viable alternative for a secure energy supply of the future," continues Stukenbrock.

Fungal infections: systemic suppression of the immune system of wheat

May 08, 2020

Kiel research team investigates how certain harmful fungi suppress the immune system of their host plants, making them susceptible to new infections

Wheat is one of the most important crops worldwide, and is the main ingredient of many staple foods. As the world's second most extensively cultivated cereal crop, approximately 20-25 million tons of wheat are produced per year in Germany alone. However, in north-western Europe, wheat production is confronted with the harmful fungus Zymoseptoria tritici, which attacks the wheat leaves and can cause serious harvest losses of up to 50 percent. Chemicals used by farmers to protect wheat against this fungus is responsible for approximately 70 percent of the total plant protection products used in Germany - and it thereby represents a major challenge to food security. On the one hand, researchers are working to breed resistant species, and on the other hand, they are developing innovative and sustainable plant protection strategies in order to keep the fungus in check. At Kiel University, the Environmental Genomics group led by Professor Eva Stukenbrock explores the molecular interactions of plant and fungus, and the resulting mutual evolutionary adaptations, among other topics. In this regard, the Kiel research team has now published a study, with support from the Canadian Institute for Advanced Research (CIFAR) and the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms" at Kiel University, among others, which investigates the mechanism of fungal infection in wheat, particularly in terms of the impact of the pathogen on the plant’s immune system. The researchers were able to show that the fungus influences the plant metabolism, changes the composition of the wheat microbiome, and furthermore that localised Z. tritici infection leads to a systemic suppression of the plant’s immune system, which makes further colonisation by the pathogen easier. The scientists published their paper today in the renowned journal Nature Communications.

Fungal infections suppress the immune system of plants
The Kiel scientists investigated the mechanisms of fungal infection using two different varieties of wheat: one which is susceptible to the fungus, and one which is resistant. In doing so, they concentrated on changes in the plant’s metabolism. In response to the fungus, the resistant plants produce antifungal metabolites, which inhibit the growth of the fungus. In addition, they produce certain substances that strengthen the cell walls of the plant cells. This makes penetration by the fungus more difficult, and helps to fight the infection. However, these mechanisms are manipulated in the susceptible wheat plants. These are unable to produce antifungal metabolites and there is no reinforcement of the cell walls during the invasion of Z. tritici. "Interestingly, these effects are not limited to the site of infection," said Dr Heike Seybold, a former post-doctoral researcher in Stukenbrock's working group and currently a scientist at the Hebrew University of Jerusalem. "We were able to show that during the course of the fungal infection, there is a systemic suppression of the immune system in certain varieties of wheat, and suspect that the fungus can cause this effect," added Seybold.

Harmful fungi change the plant microbiome
These processes can be understood based on the microbial colonisation of the wheat plant: after contact with the fungus, there are changes in the quantity and composition of the microorganisms present in the plant microbiome. "With the fungus-resistant variety, the diversity of species in the microbiome decreases as soon as the plant is infected," explained Seybold. "This means that especially the core microbiome species remain, while the immune response is increased," added Seybold. The researchers suspect that this effect is based on an evolutionary adaptation of the plant to the pathogen. In the susceptible wheat variety, the effect is accordingly not pronounced. A fungal infection in resistant plants thus causes colonisation of the microbiome by certain organisms to be prevented, and its overall composition is changed from a functional perspective, in order to fight the infection.

In a follow-up step, the researchers studied how these changes affect the susceptibility of the plants to other pathogenic organisms, for example certain harmful species of bacteria. When they initially took wheat plants that were not infected with the fungus, and infected them with the bacteria, the bacteria grew equally well in both wheat varieties, the resistant and the susceptible. "Differences in the growth of bacteria only appear if you infect both varieties with Z. tritici and the bacteria at the same time, but in separate parts of the plant," explained Seybold. In this case, the resistant variety was able to ward off both the fungus and the bacteria. In contrast, the variety, which is susceptible to the fungus was even more vulnerable to the bacteria than before. “This underlines the fact that the fungus is able to suppress the immune system of the wheat overall - regardless of where the infection occurs," continued Seybold.

The value of transdisciplinary cooperation
The new results of the CAU researchers are the product of extensive cooperation between various areas of expertise: the plant researchers at the Botanical Institute cooperated with experts for genome sequencing and specialists for the analysis of metabolic data in so-called metabolomics research - namely in Professor Andre Frankes Genetics and Bioinformatics Group at the Institute for Molecular Biosciences and the Department for Food Technology led by Professor Karin Schwarz at Institute of Human Nutrition and Food Science, both at Kiel University. It’s only through this joint effort that they succeeded in gaining valuable new insights into the interactions between crops and pathogens from three complementary scientific perspectives. "Our new transdisciplinary study is of great importance for further research into sustainable plant protection strategies," emphasised Stukenbrock, spokesperson of the Kiel Plant Center (KPC) at Kiel University for plant research. "We were able to show for the first time how a plant pathogen triggers a systemic immune response in crop plants, and can thus cause increased susceptibility to other harmful organisms," added Stukenbrock. As a result, an additional important facet of fundamental research is now known, which in future can be used to develop new protection strategies for crop production.

Stability and dynamics of the microbiome

Mar 12, 2020

Researchers from Kiel University investigate basic principles
of microbiome composition using roundworms as an example

Every multicellular creature in the world is colonized by an unimaginably large number of microorganisms and has evolved together with them in the history of life. The natural microbiome, i.e. the totality of these bacteria, viruses and fungi living in and on a body, is of fundamental importance for the entire organism: on the one hand, it performs vital tasks for the host organism, for example, from supporting resource utilization to protecting against pathogens. On the other hand, microbial dysbiosis is associated with various serious diseases in humans like diabetes, Crohn's disease or other chronic inflammatory diseases. Researchers worldwide have therefore been intensively studying the highly complex interactions of host organisms and microorganisms and their involvement in central life processes for several years.
An important approach for their better understanding is the investigation of so-called model organisms. These include the nematode Caenorhabditis elegans, which is only about one millimetre long. Due to its simple organisation and short generation time, C. elegans is well suited for evolutionary biology and microbiome research. Using this example, a research team from the Evolutionary Ecology and Genetics Group at Kiel University has now published a long-term study within the framework of the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms". It investigates the underlying factors influencing the composition of the natural intestinal microbiome of the nematode. The researchers from Kiel found out that the microbiome of the worm is strongly influenced by the microbial community of the environment and that there are strong differences between individual animals. In addition, the worm’s microbiome appears to be strongly influenced by the interactions between the microbes themselves. The results suggest that the microbiome is capable of performing the same basic functions for the host, independent of its exact composition. The researchers recently published their results in the journal Environmental Microbiology.

Individual composition of the microbiome
Researchers from the Evolutionary Ecology and Genetics group headed by Professor Hinrich Schulenburg had already presented the first systematic characterization of a natural C. elegans microbiome a few years ago. In a follow-up research project, the Kiel research team has now investigated how the composition of this microbial community assembles in the first place and how it differs from the worm's bacterial diet, i.e. the microorganisms found in its direct environment. "The worm takes up its food and thus certain parts of its microbiome from its direct environment. In the case of our study, this was a compost heap consisting mainly of rotting biomass and hence a microbe-rich substrate," said first author Dr Julia Johnke, scientist in the Evolutionary Ecology and Genetics group. "The environment is thus the source of the worm microbiome and, in a sense, offers a broad spectrum from which the microbiome can be assembled. However, the comparison of the microorganisms in the substrate and in the animals showed that the microbial community in each individual animal is individually composed and differs from the much more diverse microbial repertoire of the environment," said Johnke. "The environment is the source of the worm microbiome and in a sense offers a broad spectrum from which the microbiome can be assembled”, she added. The composition of the worm microbiome is therefore subject to environmental filtering that regulates the microbial community independently from external conditions.

An ecosystem inside the body
The Kiel researchers thus concluded that, apart from a few constants, it is always different microbes that make up the natural microbiome of the individual animals. "There is not a specific single set of bacteria that helps the worm to maintain important life functions such as food conversion or infection protection," emphasises Schulenburg, evolutionary biologist and head of the research group. "The microbiome of the nematode varies considerably from individual to individual and changes dynamically over time," continued Schulenburg. In order to understand how a stable functioning of the microbiome is maintained despite this dynamic development, the Kiel research team studied the interactions between the microorganisms in more detail: Although the microbiome interacts with the host organism, it is at the same time strongly influenced by the interplay between the microorganisms themselves.

For example, certain species of bacteria, which prey on other bacteria, can control the density of bacteria within the microbiome. To a certain extent, this creates space for various other types of microorganisms. Overall, this can result in a high species diversity within the microbiome. "Such high diversity can potentially be beneficial for the host organism," says postdoctoral researcher Johnke. "The high diversity can ensure a functional redundancy of the microbiome, i.e. that different bacterial species can, to a certain extent, stand in for each other and take over the same functions," continues Johnke. In the opposite case, the increased occurrence of dominant species within the microbiome can lead to a decrease in diversity and thus have potentially negative effects on the host organism - this case, too, can presumably take place in the microbiome of the nematode.

When investigating the microbial composition and its changes over time, scientists, as in the Kiel study, apply, among other things, the principles of community ecology. They regard the microbiome as an independent ecosystem in which, for example, different species of bacteria compete with each other, basically following the same principles as, for example, wild animals that live together in a particular habitat and regulate each other in their populations. "The consideration of the nematode microbiome as an independent ecosystem is of great value because it allows us to obtain fundamental insights into the colonization dynamics and microbial composition of a living organism," emphasises Schulenburg. "Similar to the ecosystems of the visible environment, different organisms in this microbial habitat can occupy identical niches or functions or a high species diversity can be beneficial for the stability of the entire system," continued Schulenburg. The new results thus contribute to a better understanding of the composition and dynamics of the microbiome and the associated functional consequences for the host organism.

About CRC 1182:
The Collaborative Research Centre "Origin and Function of Metaorganisms" is an interdisciplinary network involving about 80 researchers that investigates the interactions of specific microbial communities with multicellular host organisms. It is supported by the German Research Foundation (DFG) and deals with the question of how plants and animals, including humans, form functional units (metaorganisms) together with highly specific communities of microbes. The aim of SFB 1182 is to understand why and how microbial communities form these long-term connections with their host organisms and what functional consequences these interactions have. The SFB 1182 brings together scientists from five faculties of Kiel University, the GEOMAR Helmholtz Centre for Ocean Research Kiel, the Max Planck Institute for Evolutionary Biology Plön, the Heinrich-Heine-Universität Düsseldorf, the Leibniz Institute for Science and Mathematics Education and the Muthesius University of Fine Arts and Design.

An international comparative study with Kiel participation demonstrates advantages of precision therapies compared to standard treatments for certain cancers

In spite of intensive prevention and early detection efforts, colorectal cancer is becoming increasingly common, especially in industrialized nations. Health experts predict that this form of cancer globally could cause over a million additional deaths per year by 2030. This type of cancer, the second most common in Germany, is challenging because it grows without symptoms for a long time. By the time the disease is diagnosed, it is often too late for successful treatment. Given this challenge, scientists around the world are working on novel strategies to improve early detection on the one hand and to treat advanced stages of colorectal cancer better on the other. In the latter endeavour, standard treatments are generally offered to patients, but various individualized forms of therapy are gaining importance, which take particular account of the genetic predisposition of the patient.

Researchers from Kiel University, the University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, and the Avera Cancer Institute in Sioux Falls, USA, together with an international research team, have published a comparative study of American and German colorectal cancer patients, comparing standard treatment protocols with a combination of standard and individual therapy. They come to the conclusion that patients with certain forms of advanced colon cancer lived on average 16 months longer thanks to supplementary individual treatment. The researchers from the Institute for Clinical Molecular Biology (IKMB) at Kiel University, together with their international colleagues, recently published their study in the current issue of the scientific journal Cancers.

Comparison of treatment guidelines
In order to make valid statements about the effectiveness of the various treatment strategies, the research team compared disease cases from the United States to a German patient group. First, the scientists made sure that the initial situation was comparable: All patients were affected by a form of stage III or IV colorectal cancer. Given the advanced stage of colon cancer with metastases in the liver, lungs or other organs, less than 20 percent of patients had a realistic prospect of successful treatment.

"Next, we recruited a group of patients of mainly northern European descent in the United States who were very similar to German patients in terms of ancestry,“ emphasizes the Kiel study leader, IKMB scientist Dr Michael Forster. "On this basis, we identified which disease courses resulted from the different treatment guidelines in Germany and the US," Forster continues.

A total of 108 patients were analysed. On the German side, 54 patients were divided into high-risk and low-risk groups based on the so-called mutation profiles. In the high-risk group, a particular combination of mutations is responsible for a rapid progression of the disease. Such a constellation generally only occurs in a few cases and the fourth stage of the disease also occurs relatively rarely due to improved preventive care. The German patients were treated according to European guidelines for this type of cancer and survived on average for 19 months after diagnosis.

Precision medicine in cancer therapy
The American patients in the study were initially also treated according to a standard procedure, which, however, already included more treatment options than in Germany. Their average survival was 33 months. In 35 patients, the standard protocol was followed by additional treatment tailored to the individual concerned, which was based on an assessment of the genetic and molecular profile of the tumor. The scientists' hypothesis was that especially patients with advanced stages of the disease and the associated complexity of the tumor needed treatment tailored to the tumor's mutation profile. An interdisciplinary “Molecular Tumor Board”, composed of doctors and experts in molecular biology, bioinformatics and genetics, developed a specifically tailored treatment recommendation for each patient. This individual treatment may include a combination of multiple medications. The comparison of the two groups demonstrated that the individualised approach ensured that American patients survived on average for almost a year and a half longer, driven especially by improved survival of critically ill patients. Many experts see the future of cancer medicine in this more patient-oriented approach.

The present study shows the advantage of individualized forms of therapy in colorectal cancer treatment compared to standard procedures. The latter are based on empirical values from large numbers of cases and ensure the quality of treatment, but they do not always take sufficient account of the specific situation of the individual patient as a basis for decision-making when tailoring the treatment. The significantly higher life expectancy in the United States in a quasi-identical initial patient setting suggests that treatment guidelines can and should be improved across national borders. "The comparison of the treatment options, which differ significantly between the two countries, shows the great impact that personalized treatment can have on the individual life expectancy of patients," emphasizes Dr Tobias Meissner, Head of the Department of Experimental and Molecular Medicine at the Avera Cancer Institute. The work also confirms a general development in medicine, which is exemplified by the Schleswig-Holstein Cluster of Excellence "Precision Medicine in Chronic Inflammation" (PMI): In the field of inflammation research, researchers at Kiel University and its partner institutions are doing pioneering work in the development of precision medicine. Particular emphasis is placed on prevention. It is possible that individual therapeutic approaches will be effective in the future even before serious chronic diseases, including cancer or inflammatory disease, can develop.

Obesity, heart disease or diabetes could be transmissible

Jan 20, 2020

International research team with the participation of Kiel University’s Professor Thomas Bosch provides evidence that so-called "non-communicable diseases" could possibly be passed on from person to person via the microbiome

Diseases such as cardiovascular diseases, cancer or certain lung diseases are among the most common non-natural causes of death today and account for about 70 percent of deaths worldwide. They are defined by the World Health Organization (WHO) as non-communicable because they are assumed to be caused by a combination of genetic, lifestyle and environmental factors and cannot be transmitted between humans. In a new research paper, a team from the "Humans & the Microbiome" program of the Canadian Institute for Advanced Research (CIFAR), with the participation of Professor Thomas Bosch from Kiel University, is now questioning this view. The scientists provide convincing evidence that many diseases classified as non-communicable may possibly be passed on from person to person via the microbiome after all - and that the microbial colonisation of the human body, including bacteria, fungi and viruses, is centrally involved in the transmission. The researchers published the new hypothesis last Friday in the leading scientific journal Science.

A revolutionary hypothesis
“If our hypothesis is proven correct, it will rewrite the entire book on public health”, says Brett Finlay, Professor of Microbiology at the University of British Columbia and head of the CIFAR program "Humans & the Microbiome". The scientists base their theory on making, for the first time, connections between three different already proven findings: First, they have been able to show that in a wide range of diseases, from obesity and inflammatory bowel disease to type-2 diabetes and cardiovascular disease, the human microbiome shows significant changes compared to the healthy body. Secondly, they have provided ample evidence that such altered microbial compositions lead to the development of disease when transferred in laboratory experiments to an originally healthy model organism. If, for example, the intestinal microbiome is taken from an obese mouse and transferred to a healthy animal, the latter will also become overweight. Finally, they found numerous indications of a general natural transferability of the microbiome. “When you put those facts together, it points to the idea that many traditionally non-communicable diseases may be communicable after all”, says Finlay.

Researchers from Bosch's group at Kiel University have been able to prove the third aspect in particular. "If laboratory animals such as freshwater polyps are not kept individually, but rather were “co-housed” for a certain period of time in a common habitat, their microbiome first adapts to each other and then, as a result, also their phenotype," summarizes co-author Bosch, spokesperson of the Collaborative Research Center (CRC) 1182 "Origin and Function of Metaorganisms" at Kiel University. "We were able to show that the microbes pass directly from one individual to another. It is possible that this transmission of the microbiome also takes place during human coexistence, for example through intensive social contacts or in shared apartments," assumes Bosch.

Further research to validate the theory
The revolutionary new hypothesis of the CIFAR team is based on an explorative interdisciplinary exchange of the experts cooperating in the microbiome research program and their different scientific perspectives. Initiated only as a thought experiment, it quickly became clear that there are a number of clear indications from the various disciplines that make the new theory seem plausible – should it be correct, the implications for human health would obviously be extremely important. Nevertheless, the researchers stress that their hypothesis is daring and that many of the mechanisms involved are still unknown. “We still don't know in what cases transmission increases, or whether healthy outcomes can also be transmitted,” says co-author and CIFAR-Fellow Maria Gloria Dominguez-Bello, professor at Rutgers University in New Jersey. “We need more research to understand microbial transmission and its effects”, Dominguez-Bello continues.

However, there is no doubt today that there is a significant correlation between a disturbed microbiome and many diseases. Further research will show how the microbiome interacts with other influences, for example certain environmental conditions and genetic factors in the transmission of various diseases. "The new hypothesis makes it clear that we need to consider disturbances in the microbial colonization of the body as a cause of disease to a much greater extent than before, and that we also need to investigate the potential transmission pathways more closely," emphasizes Bosch. "In the coming years, this aspect will be one of the focal points of our work in our Metaorganism Collaborative Research Center," Bosch continued. The CRC 1182, which was launched at Kiel University in 2016, has been funded by the German Research Foundation (DFG) for a further four years in a second funding phase since the beginning of the year.

Original publication:
B. B. Finlay and CIFAR Humans and the Microbiome (2020): Are noncommunicable diseases communicable?Science Published on 17 January 2020DOI: 10,1126/science.aaz3834

About the Canadian Institute for Advanced Research (CIFAR):
Since its founding in 1982, CIFAR's mission has been to create interdisciplinary research teams, involving leading scientists from around the world, to address scientific topics of particular relevance to society. At present, more than 400 researchers from around 130 institutions worldwide are working on 13 interdisciplinary research projects with, for example, life science, social or technical issues. The CIFAR research teams have a total annual budget of around 28 million euros at their disposal. In its research program "Humans & the Microbiome", CIFAR brings anthropologists, biologists and other scholars together to provide biocultural context to host-microbiome interactions. They’re asking new questions about what aspects of individual and societal behaviour are critical to understanding the role of the microbiome in human health and development.

About CRC 1182:
The Collaborative Research Centre "Origin and Function of Metaorganisms" is an interdisciplinary network involving about 80 researchers that investigates the interactions of specific microbial communities with multicellular host organisms. It is supported by the German Research Foundation (DFG) and deals with the question of how plants and animals, including humans, form functional units (metaorganisms) together with highly specific communities of microbes. The aim of SFB 1182 is to understand why and how microbial communities form these long-term connections with their host organisms and what functional consequences these interactions have. The SFB 1182 brings together scientists from five faculties of Kiel University, the GEOMAR Helmholtz Centre for Ocean Research Kiel, the Max Planck Institute for Evolutionary Biology Plön, the Heinrich-Heine-Universität Düsseldorf, the Leibniz Institute for Science and Mathematics Education and the Muthesius University of Fine Arts and Design.

More information:
Research Program "Humans & the Microbiome",
Canadian Institute for Advanced Research (CIFAR):
www.cifar.ca/research/program/humans-the-microbiome
Bosch Lab, Kiel University:www.bosch.zoologie.uni-kiel.de

Rapid emergence of antibiotic resistance during standard therapy

Nov 25, 2019

Kiel research team investigates how the pathogen Pseudomonas aeruginosa becomes resistant to antibiotics during treatment of cystic fibrosis patients

Antibiotic-resistant pathogens pose one of the greatest threats to public health worldwide. In the near future, harmless bacterial infections may no longer be treatable and may again become the most common non-natural cause of death. At the same time, the available repertoire of antibacterial agents is becoming increasingly smaller as resistance rates rise. The basic mechanisms of resistance evolution, i.e. the adaptation of a disease germ to the mode of action of a drug, have been well researched experimentally. How such loss of drug susceptibility develops in individual patients in the course of standard antibiotic therapy has not yet been studied. A research team from the department of Evolutionary Ecology and Genetics at Kiel University has now investigated the evolution of resistance in the pathogen Pseudomonas aeruginosa during antibiotic treatment in a cohort of cystic fibrosis patients as an example. For the first time, they researched to what extent resistance evolves during a single course of antibiotic therapy. The researchers now found that resistance rapidly emerged in about one third of the patients. These findings were obtained within the Leibniz ScienceCampus "EvoLUNG" and the Cluster of Excellence "Precision Medicine in Chronic Inflammation" (PMI) and were recently published in the Journal of Antimicrobial Chemotherapy.

Cystic fibrosis lung infection as an example
In the study, the research team focused on a small cohort of cystic fibrosis patients. The disease, which is uncurable to date, is caused by impaired cellular water transport and leads to viscous body secretions and associated dysfunction of numerous organs. It affects the respiratory tract and lungs in particular. Frequent infections in adult patients are mainly caused by Pseudomonas. As a result, they have to be treated with antibiotics frequently or even permanently.

In order to assess whether resistance evolves in the course of a single standard treatment with two or more antibiotics, the scientists examined the bronchial secretions of the patients daily and isolated Pseudomonas bacteria. This enabled them to investigate how the bacteria adapted to therapy over a period of 14 days. "In every third patient the pathogen adapted surprisingly quickly to the administered drugs and antibiotic resistance evolved within one to three days," summarised Dr Leif Tüffers, a researcher in the Department of Evolutionary Ecology and Genetics. "The rapid evolution of resistance mainly affected newly administered antibiotics from the betalactam drug class," continued Tüffers.

Findings match evolutionary experiments
These findings were obtained in real time on patients during clinical routine therapy for the first time. They generally correspond well with experimental observations from previous laboratory experiments with the Pseudomonas pathogen. Although resistances evolve faster in the laboratory, sometimes within a few hours, the bacteria in the patient's body grow much more slowly. To date, it is not entirely clear how exactly bacteria in the patients achieve such rapid evolution of resistance to the betalactam antibiotics, including penicillin. "It is possible that this rapid adaptation to the drug occurs as a result of spontaneous, new mutations in resistance genes," said Tüffers.

In current research within the Cluster of Excellence PMI, the scientists now investigate the clinical applicability of evolution-based treatment strategies, which proved successful under laboratory conditions in the past. "The processes of resistance evolution are often comparable, regardless of whether it is a laboratory experiment with a specific single bacterium or the treatment of a bacterial infection in patients," said Professor Hinrich Schulenburg, head of the Department of Evolutionary Ecology and Genetics at Kiel University. "We therefore want to investigate in future studies to what extent, for example, the principle of collateral sensitivity, in which the formation of resistance to one antibiotic increases sensitivity to a second drug, can be used to treat lung infections," continued Schulenburg.

Kiel research team investigates which evolutionary mechanisms can be used for sustainable antibiotic therapy

One of the most serious threats to public health worldwide is posed by antibiotic-resistant pathogens. The World Health Organization (WHO) warns of the imminent beginning of a postantibiotic era in which harmless infections can no longer be treated and could once again become one of the most frequent non-natural causes of death. Decades of using various antibiotics as standard therapy have greatly reduced the spectrum of effective antibacterial drugs. At the same time, the development of new drugs is being partially reduced or completely discontinued. This is due to the rapid evolution of antibiotic resistance, which makes antibacterial drugs ineffective within short time periods. For some years now, researchers have therefore attempted to develop strategies to maintain or even improve the efficacy of existing antibiotics.
At the Kiel Evolution Center (KEC) of Kiel University, Germany, the Schulenburg lab develops and investigates evolution-based strategies with the twofold aim to eliminate bacterial pathogens and also minimize evolution of drug resistance. A promising principle that the KEC researchers apply is collateral sensitivity. This technical term describes the occurrence of advantageous, evolutionary 'costs' for the development of antibiotic resistance, which always arises when the evolution of resistance to one particular antibiotic makes the pathogens highly sensitive to a second drug. Using the bacterium Pseudomonas aeruginosa as an example, the researchers have now used evolution experiments in the laboratory to assess the stability of this principle over time and thus its suitability for sustainable patient treatment. In their most recent publication, the KEC research team was able to demonstrate that treatment efficacy depends on the order in which the antibiotics are applied and the mode of action of the used drugs. The new research results were published by the Kiel team today in the scientific journal eLife.

Does the treatment sensitivity of the bacteria remain stable?
In a previous study, the Schulenburg lab systematically investigated the efficacy of alternative antibiotic combination therapies. For these studies, they already used the pathogen Pseudomonas aeruginosa, an infectious bacterium that is particularly dangerous for patients with a weakened immune system. They were the first to demonstrate the principle of collateral sensitivity for this pathogen. Moreover, they found that the antibiotic treatments were particularly effective, when a so-called aminoglycoside antibiotic was alternated with a betalactam antibiotic, thus a penicillin-like drug. "On the basis of this preliminary work, we now wanted to find out whether this promising principle can be successfully applied under temporally changing conditions and whether the evolved high sensitivity of the germ remains stable," emphasizes Kiel professor and KEC spokesperson Hinrich Schulenburg.

In the work now presented, the Kiel researchers were able to show in comprehensive laboratory experiments that the suitability of the collateral sensitivity principle depends on several factors: In particular, the order of the antibiotics used, the evolutionary costs for the evolved resistance and also the underlying genetic mechanisms determine the treatment efficacy. "The pathogen’s ability to adapt was particularly constrained when the treatment included a drug change from an aminoglycoside to a betalactam, i.e. a penicillin-like substance," explains Dr. Camilo Barbosa, first author of the study. In this case, the bacteria were unable to adapt and went extinct as a result of the combined administration of the antibiotics. In other drug combinations, however, the pathogens were able to develop new multiple resistances. Moreover, the evolutionary costs of resistance play an important role in therapy success.

Basis for evolution-based antibiotic therapies
The new research results from the KEC scientists on the stability of collateral sensitivity may allow the development of novel and sustainable antibiotic therapies in the future. The effects of changing certain drug classes and the impact of evolutionary costs on the development of resistance impressively demonstrate the enormous potential of evolutionary principles for the design of new, sustainable antibiotic therapies. "In a next step, we plan to further develop these promising evolution-based strategies for their application on patients and here take advantage of the highly collaborative environment among basic scientists and clinicians in Northern Germany," concludes Schulenburg.

Tracking down the functions of the microbiome

Oct 29, 2019

Research team from the Kiel CRC 1182 analyses how microorganisms affect elementary functions of their host organism, using the example of nematode worms

All living creatures - from the simplest animal and plant organisms right up to the human body - are colonised by numerous microorganisms. They are thus in a functional relationship with these microbes, and together form a so-called metaorganism. The investigation of this symbiotic cooperation between host organism and microorganisms is a key challenge for modern life sciences research. The composition of the microbiome, i.e. the totality of the microorganisms which colonise a body, is well studied in numerous organisms. However, how these microbes cooperate with the host, and what role they play in its biological functions, is still largely unknown. The Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms" at Kiel University (CAU) aims to understand the communication and thus also the functional consequences of host-microbe interactions.

Researchers at the CRC 1182 have now, for the first time, presented a functional repertoire of the microbiome of the nematode (or thread worm) Caenorhabditis elegans, thereby providing new insights into the connection between bacterial properties and metabolic functions of the host. The Kiel scientists recently published their results, which could also serve as a model for the analysis of the microbiome functions in other organisms, in the ISME Journal.

Nematode microbiome provides all important nutrients
Due to its simple structure and short generation time, the nematode C. elegans is a classic model organism in biological and medical research. However, to date, the role of its microbial symbionts has been mostly overlooked. Only a few years ago, a research team from the Evolutionary Ecology and Genetics research group at CAU characterised, for the first time, the natural bacterial colonizers of this worm. The Kiel research team also obtained first evidence of a functional influence of microorganisms, for example on the stress resistance of the worm or its ability to resist pathogens. "On this basis, we wanted to gain an overview of the functional repertoire of the natural worm microbiome," emphasised Nancy Obeng, doctoral researcher in the Evolutionary Ecology and Genetics research group and CRC 1182 member. "To do so, we predicted the metabolic networks of the nematode microbiome, based on whole genome sequence data from the bacteria," continued Obeng.

For this purpose, the CRC 1182 researchers analysed the genome sequences of a total of 77 representative bacterial species from the digestive tract of the worm, and used these to infer metabolic networks of these microorganisms using mathematical modelling. This approach allowed them to predict which metabolites can arise as end products of certain available nutrients. "The conclusion of our modelling is that the microbiome of the worm is capable of producing nearly all essential nutrients for the host," emphasised Johannes Zimmermann, doctoral researcher in the Medical Systems Biology research group at the CAU and also a member of the CRC. These results were subsequently confirmed experimentally in the laboratory. "It is primarily the frequently-occurring microbial colonizers, which provide the nematode with its required nutrient components," added Obeng.

Model for functional microbiome research
Using the example of the nematode C. elegans, the CRC 1182 researchers have thus developed a model to theoretically and experimentally derive metabolic networks on the basis of whole genome sequencing data. Similar to how the nematode serves as a model system for various life processes, such as individual development or the ageing process, the methodology developed here could in future also help to determine the functional scope of the microbiome in other organisms - including humans.

"With our new approach for functional analysis of the microbiome, we have opened the door to a better understanding of the fundamental interaction of organisms and their microbial symbionts," emphasised CAU Professor Hinrich Schulenburg, head of the Evolutionary Ecology and Genetics research group and Vice-Speaker of the CRC 1182. "In the future, we intend to perform comparable functional analyses across the entire spectrum of model organisms studied in our Collaborative Research Centre here in Kiel," added CAU professor Christoph Kaleta, head of the Medical Systems Biology group. Currently, the scientists from the Kiel metaorganism CRC are applying for renewed funding from the German Research Foundation (DFG), to continue exploring the interaction of organisms with their microbial partners.

Symbiosis as a tripartite relationship

- Joint press release by Kiel University and the GEOMAR Helmholtz Centre for Ocean Research Kiel -

Investigation of viral communities of sponges allows new insights into the mechanisms of symbiosis

Sponges form an extensive animal phylum with over 7,500 species worldwide, which occur in a wide range of habitats in the ocean. A special feature of this animal phylum is their ability to filter seawater, through which these organisms obtain their food. In doing so, certain sponge species can move up to 24,000 litres through their body per day. The surrounding seawater contains a wide range of viruses - on average, one millilitre of water contains 10 million viruses. The filter-feeding lifestyle of sponges combined with the rich proliferation of viruses in the ocean therefore might suggest that marine sponges may have a similar viral composition as the surrounding water.

Researchers from the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms" at Kiel University (CAU) and the GEOMAR Helmholtz Centre for Ocean Research Kiel have now surprisingly shown that sponges possess a very specific viral sequence signature (i.e., virome), which is remarkably unique even for the individuals of a given species. Certain bacteriophages - i.e. viruses that attack bacteria - are further able to modulate the host immune system and thus protect bacterial symbionts from being digested. While viruses are typically known for their pathogenic properties, the new research findings now also demonstrate a positive influence of bacteriophages on the interaction of host organisms with bacteria. The results were obtained through international cooperation between three countries, including researchers at the universities of Würzburg, Barcelona and Utrecht. The study published today in the renowned journal Cell Host & Microbe thus sheds new light on the symbiosis between multicellular organisms and their microbial communities, which may be regulated by bacteriophages in a tripartite relationship.

An unexplored microcosm
In order to analyse the composition of the viral community of sponges, the researchers examined four different sponge species from a defined location in the Mediterranean Sea. In each case, they compared numerous individuals and different tissues of the same species with each other. "Contrary to our original assumption, each sponge individual has its own unique virome even when living right next to each other”. Therefore, no two sponges are alike with regard to their viral community," summarised Martin T. Jahn, a doctoral researcher at GEOMAR and early career researcher at the CRC 1182. "The composition of the virome is thus not primarily determined by the environment or the exposure of the tissue to the surrounding water, but is rather defined by internal factors," said the first author of the study, who collaborated with other early career researchers from four working groups at the CRC 1182.

Notably, the viruses discovered in sponges were largely unknown. "We have found almost 500 new genera of viruses in our samples," emphasised Jahn. "These viruses are completely new, and possibly only occur in sponge, and nowhere else in nature," said Jahn. This order of magnitude shows that the study of viral diversity is only just beginning.
The animal host, bacteria and phages interact with each other
The observed differences between the viral communities of sponges and those from seawater provoked the question whether sponge viruses have specific functions. The researcher team investigated the viral gene inventories and discovered genes which are similar to those of multicellular organisms, where they are responsible for interactions of certain proteins. "This surprising result awakened our special interest," said Ute Hentschel Humeida, CRC 1182 member and professor of marine microbiology at GEOMAR. "We wanted to understand why the bacteriophages have a gene encoding a protein, which we would rather expect in multicellular organisms", continued Hentschel Humeida.

In order to investigate the role of this so-called ANKp protein, they examined its impact in a model system: they expressed the protein in the bacterium Escherichia coli and investigated its effect on certain scavenger cells (macrophages) that occur in the immune system of vertebrates. The result points to a central role of the ANKp protein: it caused E. coli to be significantly less destroyed by the scavenger cells. Strikingly, the protein apparently enables the bacteriophages to interact with the animal host in that it downregulates the host’s immune response, thereby protecting the bacteria from being digested. Therefore, the scientists suggest that bacteriophages are part of a tripartite interaction of host organism, bacteria and bacteriophages, where they provide mechanisms for maintaining symbiotic co-existence.

Extension of the symbiosis concept?
The researchers at the CRC 1182 interpret the new results as a novel and important contribution of bacteriophages to the symbioses of multicellular host organisms and their microbial partners. "We suspect that bacteriophages are major players in the interaction between multicellular host organisms - including humans - and bacteria," summarised Martin T. Jahn. "Viral proteins such as ANKp may even enable this interplay of hosts and bacteria in the first place, because they allow the bacteria to evade the immune system of the host," continued Jahn. "The fundamental concept of symbiosis can therefore be understood as an interaction between three parties," concluded Hentschel Humeida. In the future, Hentschel Humeida and team will further investigate this hypothesis, which is of central importance for metaorganism research, and confirm the functional participation of bacteriophages in host-microbe symbioses.

Did microbes assist life in colonizing land?

Sep 19, 2019

Comparative microbiome study enables researchers of the Kiel based CRC 1182 to gain new insights into the course of evolution

All living organisms exist and function only in cooperation with an abundance of symbiotic microorganisms, and have developed together with them over the course of the earth's history. This central finding of modern life sciences has led researchers worldwide to analyse the highly complex interactions and long-term bonds of host organisms and microbes in ever greater detail. Gradually, they want to achieve a new functional understanding of biology and the development of life. In the analysis of the complex interactions within the so-called metaorganism, the unit consisting of a body and the totality of its microbial colonisation, in short the microbiome, scientists use techniques such as genome sequencing. These technologies make it possible to analyse genetic information from large quantities of biological sample material and, thanks to new high-throughput methods, quickly assign it to specific organisms and, in some cases, to possible functions.

Scientists from all working groups at Kiel University involved in the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms" have now compared various sequencing techniques in an extensive comparative study using various model organisms: On the one hand to assess their optimal areas of application, and on the other hand to identify possible similarities between different multicellular host organisms and their microbiomes. A surprising result of the study presented here is that organisms living on land generally have a significantly different microbiome than species living in water. The researchers interpret this as an indication that microorganisms may have played a key role in the evolutionary transition from purely aquatic life to life on land. The new research results were published last week in the renowned scientific journal Microbiome.

The microbiome and adaptation to terrestrial life
In the new study, the scientists of the CRC 1182 used the opportunity to compare the microbiomes of many different model organisms - from simple sponges to vertebrates, including humans. They examined sample material from the various subprojects of the collaborative research project for patterns in the composition of microbial communities and compared different methods of the two most important sequencing technologies. By chance, they came across an interesting observation: the microbiome of terrestrial organisms, regardless of their kinship relationships, differs significantly from those of aquatic organisms - in which all analytical techniques coincided. Terrestrial organisms have a lower diversity of microorganisms contained in their microbiome.

A possible explanation for the differences in the composition of the microbiome could be that former aquatic organisms were forced to acquire new microbial communities upon the colonisation of the land. The transition from water to land, which began about 500 million years ago, might have been dependent on a change in the microbiome. "Just as adaptation to life on land brought about gradual, but massive morphological changes, such changes apparently also took place in the terrestrial host-associated microbiome," says John Baines, Professor for Evolutionary Genomics at Kiel University. "In order to cope with the new environmental conditions, living organisms may have resorted to terrestrially adapted microbes to maintain their vital functions," Baines continues.

Choosing the right tool
In addition to these revealing findings on a possible influence of microbiota on the course of evolution, the new CRC 1182 study also provides an aid in choosing the appropriate analytical method for the investigation of a given microbial community. On the one hand, certain sequencing methods provide only a rough identity of the microorganisms present in a sample. These comparatively inexpensive methods - such as the so-called '16s rRNA gene amplicon' method - use individual marker genes from which it is possible to deduce the associated living organisms.

More complex methods such as the so-called 'metagenomic shotgun' sequencing make it possible to record and evaluate all the genetic information in a sample. For example, they can identify individual bacterial species within the microbiome and are also able to deduce microbial functions. In comparison, however, they are more cost-intensive, their informative value depends more on the specific field of application and they are therefore currently less standardised than simpler methods.

New insights into the course of evolution
In the future, the Kiel researchers, together with their international colleagues, want to understand more precisely what role microorganisms played in the transition from an aquatic to a terrestrial way of life over the course of earth's history. "There are many indications that symbiotic microorganisms have also played a role in major evolutionary transitions," stresses CRC 1182 spokesperson Professor Thomas Bosch. "It is therefore our goal to identify the specific evolutionary mechanisms that caused the diversification of the microbiome parallel to the colonization of the land," continues Bosch.

Why are we different sizes?

Sep 03, 2019

Kiel research team describes the interplay of environmental factors and internal regulation in determining the growth of an organism

The body size of a living creature has a direct impact on its fitness - from the simplest animal and plant organisms right up to human beings. The individual size or height is therefore an important criterion for the ability of an organism to succeed in the competition for resources or reproduction. We basically assume that there is similar genetic information within a species, which in theory should lead to relatively uniform body sizes. However, within specific physiological limits, the individuals of most species grow to very different sizes - thus size must also be dependent on other factors. But precisely which parameters regulate growth at the molecular level has hardly been investigated to date. Now, scientists from the Zoological Institute at Kiel University (CAU) have been able to show how environmental factors and internal regulatory processes jointly control body growth, using the example of the freshwater polyp Hydra. The Kiel researchers demonstrated that the ambient temperature activates specific molecular signalling pathways of the growth process, and is thus involved in determining size. In addition, they showed that genetic factors also utilise identical signal pathways, likewise contributing to size regulation in the cnidarians. The Kiel research team recently published their new findings in the renowned scientific journal Nature Communications.

Interplay of environmental and internal regulation
From a cellular biological perspective, the size of a fully-grown organism is the result of three variables: the duration of its growth, the absolute number of the resulting cells and the individual size of all these cells, which together make up the mature organism. In the course of this characteristic growth process, the organism must be able to measure its current size, and the attainment of its maximum size. In their study, the CAU researchers initially focused on the regulation of the number of cells of the cnidarian Hydra.

"We observed that Hydra produces up to 83 percent more cells at low ambient temperatures," explained Dr Jan Taubenheim, whose doctoral research in the field of cellular and developmental biology was incorporated in the current publication. "We also managed to identify the specific molecular signalling pathways which implement the influence of the temperature on the number of cells, and thus produce larger animals at cooler temperatures," emphasised Taubenheim, who is now a research associate at the Heinrich Heine University Düsseldorf. These so-called Wnt and TGF-beta signals are involved, for example, in embryonic development and cell differentiation. Their interaction with the ambient temperature and growth in size was previously unknown. "The Wnt signals also determine the transition from growth to a stationary phase in Hydra. Therefore, we suspect that they serve the organism as a measuring instrument to determine its own size, before it stops growing," said Dr Benedikt Mortzfeld, who also obtained his doctorate in cellular biology at the CAU, and is currently employed as a research scientist at the University of Massachusetts Medical School in Worcester.

The influence of genes
In addition to the ambient temperature, certain genetic information also contribute to size regulation in cnidarians. Genes that are responsible for the so-called insulin signalling pathway jointly determine the growth, among other things by controlling the number of cells during the growth phase. In a functional gene analysis, the Kiel research team was also able to show that switching off the genes responsible for this signalling pathway led to body sizes up to 41 percent smaller in the polyps. Thus, an important role in the cellular regulation processes of growth is also played by the genetic information. "Environmental factors and genetic factors take effect one after another in a multi-step process, in a fixed hierarchical sequence, and rely on the same cellular regulatory mechanisms," summarised Professor Thomas Bosch, spokesperson of the CAU Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms". "Thus they together control cell number and size as well as the duration of the growth phase, and through their interplay facilitate great variability, which results in very different body sizes of the adult organisms," continued Bosch.

Size regulation - a common principle?
The new findings on regulating size growth in the model organism Hydra contribute towards identifying universal principles in multicellular organisms. Certain similarities in the signalling pathways lead the researchers to suspect that different organisms incorporate the influences of environment and genetics in a very similar way in their internal size regulation. The next important step will be to also investigate the influence of bacterial colonisation of the body on the underlying control processes. "We suspect that the symbiotic microorganisms of the body are also inextricably linked with the regulation of individual development and thus growth in size of an organism," said Bosch. In future, the scientists want to examine this possible involvement more closely in the framework of the CRC 1182, in order to gain a better understanding of size regulation in organisms, summarised Bosch.

Coincidence or master plan?

All living things - from the simplest animal and plant organisms to the human body - live closely together with an enormous abundance of microbial symbionts, which colonise the insides and outsides of their tissues. The functional collaboration of host and microorganisms, which scientists refer to as a metaorganism, has only recently come into the focus of life science research. Today we know that we can only understand many of life’s processes in connection with the interactions between organism and symbionts. The Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms” at Kiel University (CAU) aims to understand the communication and the functional consequences of host-microbe relationships.

A key issue for the researchers at the CRC 1182 is how the composition of an organism’s microbiome forms during its individual development. It is still unclear as to whether the microbial community composition is more governed by a functional selection process or if random processes dominate. In order to examine the microbiome composition, a research team from the CAU’s CRC 1182 and the Max Planck Institute for Evolutionary Biology in Plön (MPI-EB) has now applied the theory of the so-called “neutral metaorganism” to an entire spectrum of model organisms, from very simple creatures to complex vertebrates. The scientists from Kiel and Plön published their findings yesterday in the journal PLOS Biology.

The null model of evolutionary theory

Theoretical models offer one way to make the highly complex, individual microbiome composition manageable. A fundamental model in evolutionary research is the so-called neutral null model. This is used to predict how populations would develop without any selection pressure whatsoever. The research team at the CRC 1182 has now applied this model to several model organisms from threadworms to house mice and compared the predictions with experimentally collected data. “Theory and experimental data match surprisingly well for many organisms. The predicted composition in the house mouse, for example, is found in the actual microbial species community,” summarised Dr Michael Sieber, research associate at the MPI-EB and member of the CRC 1182. “It is possible that selection plays a lesser role in the microbiome’s composition than we previously assumed, while this does not mean that the microbiome has no important functions for the organism, it could be an indication that many different compositions of the microbiome can perform these functions equally well. And which specific composition actually forms in a single organism is then driven by chance.”

A map for further exploration of the microbiome

The researchers did notice some significant deviations between the neutral model and the real compositions of the microbiome, however. For example, individual bacterial species in the mouse microbiome did not match the neutral prediction. And the microbial species composition of the Caenorhabditis elegans thread worm did not match the neutral model at all.

“We assume that these deviations between model and reality could indicate specific functions of certain microorganisms,” Sieber emphasised. Investigating the systematic deviations from the neutral model therefore holds the potential to discover key functions of certain bacterial species within the microbiome.

First explanations for the deviations from the neutral model are already being discussed. Some non-neutral bacteria in the mouse microbiome, for example, are involved in digestion and their presence may therefore be the result of a targeted selection process. On the other hand, Caenorhabditis elegans, with its very fast generational change, might not live long enough to develop a stable, mainly neutral composition of its microbiome. “The model of the neutral metaorganism therefore provides an important theoretical basis for further functional analyses of microbiome compositions across the entire spectrum of the model organisms investigated in our Collaborative Research Centre,” said CRC 1182 spokesperson Prof. Thomas Bosch.

How antibiotic resistance persists thanks to selfish genetic elements

Jun 13, 2019

Kiel research team shows mechanisms which enable bacteria to maintain resistance, even under non-selective conditions

Parts of the genetic information of many microorganisms are located on so-called plasmids. These are genetic elements which consist of a single DNA ring, and can reproduce independently of their host. Most bacteria carry plasmids as they enable them to acquire new genetic information by a process that is termed horizontal gene transfer. During this process plasmids can supply bacterial cells with novel genetic material, and also transfer it across the boundaries of other bacterial species. Thus, this process allows bacteria to quickly adapt to changing environmental conditions, which is particularly an advantage for bacterial pathogens. However, plasmids aren’t available "for free" for the host organism, as they use the host cells’ resources for their energy requirements and reproduction. Therefore, scientists have assumed that plasmids are only hosted by bacteria for as long as they can provide an evolutionary advantage. A research team from the Institute of General Microbiology at Kiel University (CAU), together with colleagues from the Israeli Ben-Gurion University of the Negev, have demonstrated that this is not always the case: Using the model organism Escherichia coli, a bacterium which frequently occurs in the intestine of various vertebrates, the scientists in a research project of the Kiel Evolution Center (KEC) were able to show that plasmids can survive permanently in bacteria, even without an apparent benefit for the host. However, in the long term, this enables bacteria to retain a potential benefit for rapid evolutionary adaptation in fluctuating environments. The Kiel research team published their findings today in the renowned journal Nature Communications.

How plasmids outlast non-selective conditions
Positive selection pressure ensures that certain plasmid functions persist when beneficial for the host. Such an external selective pressure for adaptation would be, for example, the introduction of an antibiotic. Here, the bacteria benefit from the resistance genes carried by the plasmids that provide antibiotics resistance to the cell. To date, it was assumed that plasmids are also a burden for the bacterial cell, and therefore only exist for as long as they are needed. If the bacteria are no longer exposed to the antibiotics, and therefore the selection pressure is no longer present, the plasmids should theoretically be slowly lost and become extinct.

However, as diverse plasmids are highly abundant in nature, this assumption cannot be realistic. To find out what actually happens to plasmids without selection pressure - i.e. without the antibiotics - the Kiel research team conducted an evolutionary experiment. For this purpose, the team monitored the bacterium Escherichia coli for a total of 1,000 generations. They examined how a certain plasmid - which was previously unstudied, but known to occur in numerous bacterial hosts - behaves in the absence of such selection pressure - i.e. where the host obtains no functional advantage from its existence.

"Our research results show that the frequency of plasmids decreases without antibiotics, but that they can survive at a low and stable level," explained Tanita Wein, doctoral researcher in the Genomic Microbiology working group at the CAU and first author of the study. "With these findings, we deliver a new, evolutionary explanation for the ubiquitous occurrence of plasmids in nature" said Wein.

An advantage for some, and a disadvantage for others
In order to also investigate the influence of environmental conditions on the survival of the plasmids, the researchers compared the effects of different ambient temperatures: on the one hand, the optimum temperature for the prosperity of the host bacteria of 37° C, and on the other hand, stress-inducing conditions of only 20° C. The results of this experiment showed that the plasmid frequency decreased slower at cold temperature compared to their preferred temperature range. Thus, the survival of plasmids in bacteria depends not only on positive selection for the plasmid function, but is also strongly influenced by the environmental conditions. "We show that unfavourable conditions for the bacteria may be favourable for the plasmid persistence as the plasmids may reproduce more efficiently," emphasised the microbiologist Wein. Therefore, the survival of the plasmids may be a process that is intrinsically controlled, and is not necessarily associated with an advantage for the organism as a whole," explained Wein.

Better understanding of the rapid spread of resistance
Another important aspect was discovered by the Kiel research team, which is also supported by the DFG priority programme (SPP) 1819 "Rapid evolutionary adaptation", when they exposed the bacteria to antibiotics after the experiment under non-selective conditions. Even a single dose caused all of the following generations of bacteria to have 100 percent resistance to the drug. In such a case, one speaks of an "evolutionary bottleneck", through which figuratively speaking only the insensitive individuals may progress. Thus, the new research findings show that in the course of evolution, the stable survival of the plasmids ensures that the antibiotic resistance of the bacteria can remain latently present, even if the bacteria had not previously come into contact with the antibiotic substance. "Our findings based on the example of a specific plasmid type therefore offer promising approaches for future research on the role of plasmids in bacterial rapid adaptation to fluctuating conditions," summarised Professor Tal Dagan, KEC member and head of the Genomic Microbiology working group.

About the KEC:
The Kiel Evolution Center (KEC) is an interactive platform at Kiel University that aims to better coordinate evolutionary researchers in Kiel and surroundings. Furthermore, under the key term of "Translational Evolutionary Research", specific bridges should be built between fundamental research and practical applications. Alongside the promotion of science, the focus of the Kiel Evolution Center also expressly includes teaching and public relations work. In addition to CAU, there are researchers involved from the Helmholtz Center for Ocean Research Kiel (GEOMAR), the Max Planck Institute for Evolutionary Biology in Plön (MPI-EB) and the Research Center Borstel (FZB), Leibniz Center for Medical and Life Sciences.

Over-fed bacteria make people sick

May 15, 2019

In a new hypothesis, a CRC 1182 research team suggests that inflammatory diseases are caused by an over-supply of food, and the associated disturbance of the intestine’s natural bacterial colonisation.

Since the end of the Second World War, along with the growing prosperity and the associated changes in lifestyle, numerous new and civilisation-related disease patterns have developed in today's industrialised nations. Examples of the so-called "environmental diseases" are different bowel inflammations like Crohn's disease or ulcerative colitis. Common causes include disruptions to the human microbiome, i.e. the natural microbial colonisation of the body, and in particular of the intestine. To date, scientists have explained this disrupted cooperation between host body and microbes with different hypotheses: for example, they postulated that excessive hygiene, the intensive use of antibiotics, or certain genetic factors permanently disrupt the microbiome, thus making people vulnerable to illnesses. However, these explanation attempts have so far been incomplete. A team from the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms” at Kiel University (CAU) has now formulated a new and more comprehensive ecological-evolutionary theory on the development of environmental diseases. The Kiel researchers suggest that an unnatural and particularly comprehensive nutrient supply decouples bacteria from their host organisms, and thus destroys the delicate balance of the microbiome. The, to some extent, over-fed bacteria in the gut thus promote disease development. The Kiel scientists published this fundamental new approach towards a more complete explanation of environmental diseases yesterday in the journal mBio.

The origin lies in the oceans

The starting point for the Kiel research team was the ecology of marine habitats: research on coral and algae dying off, and the associated effects on important ecosystems in the oceans, suggests that in addition to other factors such as climate change or overfishing, the nutrient conditions in the seawater may be the cause of the problem. As soon as there is an oversupply of food due to human influences, bacteria living in a community with corals begin to decouple from their hosts. They then no longer feed off the metabolic products of the host, but prefer the richer nutrient supply of the surrounding waters. The balance of the coral microbiome is disrupted because of the exodus of its symbiotic partner, and diseases occur as a result. "In this connection between nutrient availability and the balance of bacteria-host relationships, we see a universal principle which goes way beyond the very specific example of corals," explained Dr Tim Lachnit, research associate at the CRC 1182 and first author of the study. "In studies of our model organism, the freshwater polyp Hydra, we were able to experimentally confirm this connection," continued Lachnit. These small cnidarians also showed clear signs of disease as soon as their normal nutrient uptake was disturbed and an over-supply of food was available instead.

What do corals and cnidarians have to do with people?

With a high degree of probability, the knowledge gained in the experiment can also be transferred to human health. Similar to in seawater, or in the simple body cavity of a freshwater polyp, which during the course of evolution has decoupled from its external environment and a direct food supply, the nutrient supply in the human gut is also changing along with the civilisation-induced changes in eating habits - towards an unbalanced, energy-rich and low-fibre diet. In addition to direct negative health consequences, a permanently high, easy to process supply of nutrients not only affects the human metabolism it feeds, but also the bacterial colonisation of the intestine, which is also "fed". The microbes switch from the metabolites of the host as their staple food to the abundantly available nutrients from the human food and thus decouple from their interactions with the host organism. "This over-feeding of the bacteria promotes their growth as a whole, and certain species of bacteria proliferate to the detriment of other members of the microbiome in an increased and uncontrolled manner," emphasised Professor Thomas Bosch, spokesperson of the CRC 1182. "Thus, along with the change in the composition of the bacterial colonisation, the interactions between bacteria and host organism also change, and a serious maladaptation - known as dysbiosis - occurs," explained Dr Peter Deines, research associate at the Kiel metaorganism CRC.

Other civilisation-related factors increase this imbalance of the microbiome. The elimination of periodic fasting resulting from food sources not always being available, the only very rare occurrence of diarrhoea leading to episodic reductions of the intestinal bacterial colonisers and the diet-related impoverishment of the microbial diversity in the gut are just a few examples. The first two of these represent very fundamental mechanisms, which since the early development of mankind right up to the pre-industrial era enabled the microbiome to return to a normal state at regular intervals, and thus regain a healthy and natural composition.

Does the microbiome heal itself?

The "over-feeding hypothesis" proposed by researchers from the Kiel CRC 1182, in close cooperation with the CAU Cluster of Excellence "Precision Medicine in Chronic Inflammation", offers valuable approaches for further research, right through to potential transfer to future treatments: to date, scientists were particularly looking for ways to correct a disturbed microbiome through external interventions such as probiotics, i.e. the addition of certain types of helpful bacteria, or even faecal transplants to restore the balance. Now, the ecological-evolutionary perspective has added another dimension. More than ever before, it incorporates the natural ability of the microbiome to readjust itself, and to restore a healthy composition. Therefore, future research approaches lie in the specific mechanisms that balance the microbiome, and the question of whether the "overfeeding" of the bacteria can be reduced by changed eating habits. "An interesting question will be whether the original evolutionary processes which ensure the balance of the microbiome also have therapeutic potential," said Lachnit. "In the future we will, for example, not only consider the known health benefits of fasting, but also its effects on the composition and function of the microbiome, and thus on the development of inflammatory diseases," continued Lachnit.

Original publication:
Tim Lachnit, Thomas CG Bosch & Peter Deines (2019): Exposure of the host-associated microbiome to nutrient-rich conditions may lead to dysbiosis and disease development – an evolutionary perspective. mBio Published on May 14, 2019DOI: 10.1128/mBio.00355-19

Intestinal microbiota defend the host against pathogens

Mar 01, 2019

Research team from the Kiel CRC 1182 examines the role of the intestinal microbiome in fighting infections, using the nematode model Caenorhabditis elegans

From single-celled organisms to humans, all animals and plants are colonised by microorganisms. As so-called host organisms, they accommodate a diverse community of symbiotic microorganisms, the microbiome, and together with them form the so-called metaorganism. The interactions between host and microbes exert a significant influence on diverse functions and health of the host organism. Scientists from the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms” at Kiel University (CAU) are investigating these complex interactions, and attribute an important role in the defence against pathogens to the microbiota. To do so, they use various experimental model organisms, i.e. living organisms which allow investigation of the interaction with their bacterial symbionts under laboratory conditions. A research team from the department of Evolutionary Ecology and Genetics at CAU has examined the function of the natural intestinal microbiome using the nematode (round worm) model Caenorhabditis elegans. They discovered that the natural C. elegans microbiome plays an important role in the defence against infections, and that certain bacteria produce a compound with a clear antimicrobial effect. In future, the results of the Kiel scientists could help to better understand the functions of the intestinal microbiome as a whole, and in particular its effects on the colonisation of the digestive tract by pathogens. Their study was published today in the scientific journal Current Biology.

Direct and indirect protection against infection
The Kiel team laid the foundation for the current research results a few years ago, when it presented the first systematic analysis of the natural worm microbiome. This investigation led to a detailed knowledge of the composition and the dominant species of the intestinal microbiome of the worm. At that time, the researchers hypothesised that the natural microbiome benefits host fitness, for example by protecting the host against pathogens. To gain a better understanding of the function of the worm microbiome, the researchers have now examined how individual bacteria from the former study affect the fitness of the host during pathogen infection. In doing so, they identified two distinct modes of action.

"On the one hand, we were able to determine a direct protective effect of certain bacteria against a pathogen," said Dr Katja Dierking, research associate in the department of Evolutionary Ecology and Genetics at CAU, and principle investigator in the CRC 1182. "Microbiota bacteria of the genus Pseudomonas inhibit the growth of the nematode specific pathogen Bacillus thuringiensis, if you put them in direct contact with each other," continued Dierking. In addition, the study of other microbiota bacteria of the genus Pseudomonas revealed an indirect effect: although they do not inhibit the growth of the pathogen directly, they nevertheless protect the worm against its harmful effects, likely through indirect, host-mediated mechanisms. The researchers found a total of six bacterial isolates in the natural microbiome which are involved in the defence against infections: two of them protect the worm directly against pathogens, and four of them indirectly.

How intestinal bacteria inhibit the growth of pathogens
Another special feature of the new Kiel study is that it not only describes the infection-inhibiting effect of individual bacteria of the worm’s microbiome, but was also able to identify an underlying molecular mechanism. Using genomic and biochemical analyses, the scientists from the Kiel CRC 1182 in collaboration with scientists from Goethe University Frankfurt were able to identify an antibacterial compound that is produced by the two Pseudomonas microbiota bacteria, which protect the worm by directly inhibiting pathogen growth. "The Pseudomonas bacteria produce a so-called cyclic lipopeptide," explained Kohar Kissoyan, first author of the study and doctoral researcher in the Evolutionary Ecology and Genetics group. "This chemical compound exerts a direct inhibitory effect on the pathogen, and thereby suppresses its further growth," continued Kissoyan.

How can we utilise the new findings?
The new results of the Kiel team establish C. elegans, which is a standard model organism studied in numerous research laboratories throughout the world, as experimental system to explore the various functions of the natural intestinal microbiome. Next, Dierking and her research team want to conduct a detailed investigation of the mechanism of action of the antibacterial compound identified in the worm’s intestinal microbiome. The goal of the CRC 1182 is to understand the interactions of the various bacteria of the microbiome with the host organism, but also with each other. In the long-term, the Kiel researchers hope that the gained knowledge will help in the development of therapeutic strategies to treat diseases related to disturbances of the intestinal microbiome, e.g. through the targeted use of probiotics, i.e. specific beneficial bacterial cultures. Currently, the Kiel metaorganisms CRC, which started in 2016, is applying for a second funding period as of 2020 at the German Research Foundation (DFG).

Original publication:
Kohar Kissoyan, Moritz Drechsler, Eva-Lena Stange, Johannes Zimmermann, Christoph Kaleta, Helge Bode and Katja Dierking (2019): Natural C. elegans microbiota protects against infection via production of a cyclic lipopeptide of the viscosin group Current Biology Published on February 28, 2019DOI: 10.1016/j.cub.2019.01.050

Selfish chromosomes make harmful fungus vulnerable to attack

Feb 12, 2019

Members of Kiel Evolution Center discover fundamentally new traits in the inheritance mechanisms of a plant-damaging fungus

Wheat is the world's second most extensively cultivated cereal crop, and in many countries an indispensable ingredient of essential staple foods. In Germany alone, 20-25 million tons of this grain are harvested per year. However, wheat cultivation in north-western Europe faces a fungal pest, which in extreme cases can cause losses of around 50 percent of the harvest: the fight against the fungus Zymoseptoria tritici is therefore of fundamental importance for food security. Disease management has so far mainly occurred in the conventional way through the widespread use of fungicides - with all the associated disadvantages for the environment and consumers. Because the fungus is becoming more resistant to fungicides and, conversely, there are no wheat varieties that are completely resistant to the pest, scientists at Kiel University (CAU) together with colleagues worldwide are intensively researching sustainable ways to keep the fungus in check.

Translational Evolutionary Research
At the CAU, the Kiel Evolution Center (KEC) in particular is working on applying evolutionary biological principles and making them usable, among other things, for pest control. An important step in this direction has now been taken by a KEC research team, together with the Max Planck Institute for Evolutionary Biology in Plön (MPI-EB), through their investigation of the basics of inheritance in this harmful fungus, and thereby also potential ways to combat it. The Kiel researchers discovered that the so-called meiosis, i.e. the maturation division of germ cells and the associated multiplication of genetic information, occurs differently in Zymoseptoria tritici than previously thought. This fungus has additional, unpaired chromosomes that can pass on genetic information to all their offspring and not just half of the following generations. "We have found that the chromosomes, but not the fungus as a whole, gain an evolutionary advantage through this type of inheritance," emphasised Dr Michael Habig, first author of the study and research associate in the Environmental Genomics group at the CAU Botanical Institute. "Only the chromosomes themselves benefit by passing on their characteristics to all descendants, and thus in a figurative sense they act egoistically," continued Habig. The researchers described this phenomenon in Zymoseptoria tritici for the first time, and recently published their results in the journal eLife.

Meiosis - an old acquaintance from biology class?
At the centre of the newly-described inheritance process is meiosis, which is a key step in sexual reproduction, and apparently takes place fundamentally differently in this fungus than previously thought. In normal so-called Mendelian inheritance, it serves to combine the different maternal and paternal chromosomes in the form of so-called homologous chromosomes, and pass these on to the descendants. In this way, the offspring inherit half of their genetic characteristics from both the mother and father. In contrast, meiosis seems to take place differently in Zymoseptoria tritici - especially regarding the so-called supernumerary chromosomes, which cannot combine with the relevant paternal or maternal counterpart. These unpaired chromosomes are thus inherited exclusively from either the mother or the father. The researchers were able to demonstrate that the maternal supernumerary chromosomes are passed on to all descendants, and not as expected only half of the descendants. "The driving force behind this strategy is the so-called meiotic drive, which ensures the increased transmission of chromosomes to the next generation," emphasised Professor Eva Stukenbrock, head of the Environmental Genomics group, which is jointly based at the CAU and the MPI-EB, and board member of the KEC. "This alternative method of inheritance was already known from other organisms. We could now prove it in Zymoseptoria tritici, and have found very many of the chromosomes involved in this meiotic drive," continued Stukenbrock.

A potential gateway to combating wheat pests
For the organism as a whole, inheritance through supernumerary chromosomes seems to be mainly a negative process. Why the fungus has nevertheless retained this in the course of evolution, over a long period of time, has not yet been fully understood. On the one hand, it inhibits the fungus’ ability to infect wheat, but on the other hand possibly increases its ability to adapt to changing environmental conditions. However, the Kiel researchers particularly see the chromosomes’ egotistical strategy as offering potential for new means of combating the harmful fungus in future. "Perhaps we will be able to introduce specific genetic information into the fungus through this special type of inheritance, which could substantially reduce its harmfulness to wheat," Habig said optimistically. "In doing so, one could take advantage of the fact that all offspring will be equipped with the corresponding genetic information," added Habig. The methods required to do this, such as so-called genome editing, are currently being intensively researched worldwide. So in future, the principle discovered at the KEC could help to permanently protect wheat plants against attack by Zymoseptoria tritici.

Understanding nutrient cycling in the low-oxygen ocean

Joint press release by Kiel University and the GEOMAR
Helmholtz Centre for Ocean Research Kiel

Kiel research team develops basis for quantifying the nitrogen cycling in oceanic oxygen minimum zones

In the world's oceans, there are several large oxygen-depleted areas that scientists refer to as oxygen minimum zones (OMZs). These oceanic regions can encompass millions of square kilometres, and particularly occur where an intense ocean current and prevailing wind direction meet a broad coastline perpendicularly. Among other things, these flow conditions cause coastal upwelling, i.e. the upward movement of nutrient-rich deeper water. This in turn promotes the mass occurrence of oxygen-consuming microorganisms in the layers of water below the surface, which reduces the level of oxygen in the ocean. Such conditions occur, for example, in the Pacific Ocean off the west coast of South America, in line with Peru. A particularly extensive OMZ has formed here. A research team from the Collaborative Research Center 754 (SFB 754) "Climate-Biogeochemistry Interactions in the Tropical Ocean", a cooperation between Kiel University (CAU) and the GEOMAR Helmholtz Centre for Ocean Research Kiel, investigated the foraminifera, which are unicellular shell-forming microorganisms occurring throughout the ocean, in a new physiological study. Some species of foraminifera are adapted to oxygen-depleted environments as in the Peruvian OMZ. In this way, the scientists could improve our understanding of their metabolic processes, and thus extend the basis for quantifying the nitrogen cycle in the low-oxygen ocean. The researchers published their results in the journal Proceedings of the National Academy of Sciences (PNAS) yesterday.

The respiration of foraminifera
The Peruvian OMZ extends vertically from just below the water surface down to about 600 meters in depth. Depending on the depth of the water, little or no oxygen is present. These living conditions favour organisms which thrive either in the absence of oxygen or at varying levels of oxygen, such as various types of foraminifera. Depending on availability, they can "breathe" both oxygen as well as nitrate. As such, nitrate respiration goes hand in hand with the process of denitrification: this is the conversion of nitrate present in the water into molecular nitrogen in the absence of oxygen. The mass occurrence of foraminifera in the OMZ suggests that they play an important - but previously difficult to quantify - role in the nutrient cycle of these marine regions. “To better understand the role of foraminifera in the nutrient budget of the OMZ, we examined more closely the relationship between growth and denitrification rate of these organisms," explained Professor Tal Dagan from the Institute of General Microbiology at the CAU and co-author of the study.

Foraminifera prefer nitrogen to oxygen
The researchers determined the relationship between the metabolic activities of foraminifera and their size - or more precisely, the volume of their cells. In doing so they discovered that the studied OMZ foraminifera become bigger with increasing nitrate concentrations even in the absence of oxygen, and with that increasing cell volume they can also convert more nitrate. In contrast, the previous assumptions regarding the physiology of unicellular organisms with a nucleus, including foraminifera, suggested that the organisms in the OMZ should actually be smaller: with the decrease in oxygen supply, their metabolism should only be maintained with a smaller volume to surface ratio of their cells. Now, the Kiel scientists were able to resolve this contradiction: the analysed microorganisms from the OMZ do not prefer an environment with oxygen, as previously assumed. Instead, their primary metabolic pathway is nitrate respiration. "In fact, our investigations show that the foraminifera in the OMZ become bigger with increasing nitrate concentrations," said CAU marine biologist and co-author Dr Alexandra-Sophie Roy. "It seems that foraminifera do not prefer an oxygenated environment as previously assumed, or that they only switch to nitrate respiration in case of emergency. It rather seems that an environment without any oxygen is their natural preference," continued Roy.

An oxygen minimum zone in a test tube
In order to examine the metabolic pathways of the organisms, the researchers had to incubate living foraminifera in the laboratory. They obtained the organisms from sediment samples from Peruvian research area, via core sampling from the ocean floor. "Since the foraminifera in the Pacific off Peru have very specific living conditions, we had to simulate these parameters in the laboratory," said Dr Nicolaas Glock, leader of this study, from the Marine Geosystems research unit at GEOMAR, and a member of the SFB 754. "To reproduce the conditions, I worked in a cold room mimicking the ocean temperatures at 300 meters, and also precisely adjusted the salinity, nitrate and oxygen content of the experimental media”, continued Glock. He used a procedure that removes the oxygen from the seawater in a tiny glass container, a so-called cuvette, to simulate the oxygen depletion in the OMZ. He surrounded the investigated water samples containing living foraminifera with a vitamin C solution that was separated from the specimens by a thin silicon membrane. The oxygen slowly diffused through the membrane and was trapped within the Vitamin C solution. In this way, it was possible to reproduce the environmental conditions in the OMZ in the laboratory, and thereby characterise the physiological adaptations of the foraminifera to anoxia.

The influence of marine nutrient cycles on the fishing industry and climate
In the future, the theoretical basis for denitrification rates of foraminifera, described by the Kiel researchers could help to develop more accurate models of the nutrient cycles. In particular, nutrient cycling plays an important role in the oxygen minimum zones: accurate models for nutrient cycling are fundamental for our understanding of marine primary production, such as plankton growth. This in turn is the basis of the food chain in the ocean, and ultimately of all fishing yields. As such, OMZs represent only about 0.1 percent of the global ocean surface, but yield around 18 percent of global fishing. Since the OMZs may have expanded due to human influence in the last 60 years, a detailed understanding of the nutrient cycle in these regions is of particular importance. In the context of climate change, it is also becoming increasingly important to be able to quantify climate-relevant substances and their levels in the OMZs more precisely in the future. "Only with models based on realistic quantities can future predictions be made about the quantities of the important nutrient nitrate in the low-oxygen ocean, or the amount of CO2 release taking place there," said Professor Andreas Oschlies from GEOMAR, and speaker of the SFB 754. "With their newly-presented research, the scientists involved have established a very good basis for better forecasts, which now also takes into account the important role of a widespread group of organisms in the nitrogen cycle," continued Oschlies.

About the CRC 754:
The Collaborative Research Centre 754 (SFB 754) "Climate and Biogeochemical Interactions in the Tropical Ocean" was established in January 2008 as cooperation between Kiel University and the GEOMAR Helmholtz Centre for Ocean Research Kiel. The SFB 754 investigates changes in ocean oxygen content, their potential impact on oxygen minimum zones and the consequences for the global interaction of the climate and biogeochemistry of the tropical ocean. The SFB 754 is funded by the German Research Foundation (DFG) and is in its third phase (2016-2019).

Structure of a central metabolic enzyme determined

Feb 01, 2019

Kiel research team provides key to functional understanding of the human mARC1 enzyme

One of the primary challenges for every living being is to determine the usefulness or harmfulness of ingested substances. In the case of food intake, for example, highly-specialised enzymes are used, which assist with the production of energy from chemically complex food substances. On the other hand, completely different enzymes are involved in breaking down certain non-usable or toxic foreign substances: similar to the immune system, they act as a protective barrier for the body to prevent the absorption of pollutants. In contrast with the specialised digestive enzymes, they are very non-specific, since they need to respond to a wide range of different chemical compounds in order to convert these to excreta. An example of such an enzyme in the human body is the so-called mARC1, which is involved in nitrogen conversion. A Kiel research team described it for the first time around ten years ago, and suspected that it has a special significance for physiology. Now, scientists from the Institute of Pharmacy and the Centre for Biochemistry and Molecular Biology at Kiel University (CAU) have succeeded in producing a high-resolution structural image of the mARC1 enzyme, using a special X-ray crystal structure analysis. This precise depiction of its spatial structure and the molecules contained inside provides the basis for a better functional understanding of the mARC1-controlled metabolic processes. The researchers, who are part of the CAU priority research area "Kiel Life Science" (KLS), recently published their results in the scientific journal Proceedings of the National Academy of Sciences (PNAS).

The Kiel researchers suspected that the enzyme plays a significant role in the metabolism, due to its universal occurrence: it is found not only in every human being, but also in all higher forms of life throughout the animal and plant kingdom. In nitrogen conversion, it triggers biochemical processes that essentially consist of either a reaction or the corresponding reverse reaction - depending on whether it binds or releases oxygen. With these fundamental mechanisms, it can play an important role in the control of pollutants: because nitrogen compounds in some cases produce either particularly toxic or mutagenic degradation products, the enzyme can contribute to their detoxification. At the same time, mARC1 is a special case, since it is only the fourth molybdenum-containing enzyme to be identified in the human metabolism - the xenobiotic metabolism is otherwise mainly characterised by enzymes containing iron.

"We have now been able to look inside the active centre of mARC1 in detail for the first time, and determine how it functions on the basis of its structure," said Professor Axel Scheidig, Director of the Centre for Biochemistry and Molecular Biology (BiMo) at the CAU. "The enzyme can be very effective in reducing pollutants which accumulate in the cell as metabolic products of nitrogen conversion," continued Scheidig. However, depending on the bonds it forms, mARC1 can also work in reverse. Then a toxic effect may occur, due to the conversion caused by the enzyme.

The key to determining the detailed structure was a so-called X-ray crystal structure analysis, which the Kiel research team carried out in cooperation with colleagues from the Deutsches Elektronen-Synchrotron (DESY) in Hamburg. It allowed the very weak signal of the atomic structure itself to be amplified by X-rays, through the interaction of numerous coherently-phased molecules. In this way, the researchers were able to make the structure of the enzyme visible, using the crystal made up of billions of individual molecules. However, for successful crystallisation, they first had to clean the protein molecules of the enzyme and link them with another protein in a lengthy optimisation process, without affecting the functioning of the enzyme while doing so. "We have worked on finding a way to visualise the enzyme structure for about ten years," emphasised Scheidig. "The highly precise depiction of the detailed structure of mARC1 which is now available opens the door to potential exploitation of its functions," he continued.

Now, in further research, the whole spectrum of metabolic processes controlled by mARC1 can be explored, including the organic and inorganic compounds produced. In addition, there is also a second, very similar enzyme, mARC2, whose previously-unknown structure can now also be investigated in detail. The goal of the future work is especially to explore the therapeutic potential of the two closely-related enzymes.

In addition to their importance for nitrogen metabolism, the mARC enzymes are also involved in the conversion of toxic plant substances such as alkaloids, as found in plants like the common ragwort. Here too, it is possible that the chemical reaction produces both harmless and harmful degradation products. Ultimately, the targeted use of enzymes allows the development of novel medicines: for example, the enzymes are involved in the activation of newly-developed blood thinning and anti-cancer drugs. This principle also originated from the working group of Professor Bernd Clement from the Institute of Pharmacy. For future developments, it is conceivable that with the help of mARC, the conversion and thereby the activation of an active substance may be controlled so that it already works in the digestive tract, and does not first have to be absorbed into the bloodstream. Researchers also refer to such medications with delayed activation in the body as "prodrugs". "From a pharmaceutical point of view, by applying this principle, we hope for an increased effectiveness, and potentially reduced side-effects," highlighted Clement.

The genetic profile of mARC1 plays a central role in this further research: here, the Kiel scientists were able to close a knowledge gap, as previous bioinformatic methods were only able to provide an incomplete picture. "We have also identified the genes that underlie the formation of the enzyme in humans," emphasised Clement. "On this basis, we will carry out a systematic functional analysis of the mARC1 enzyme in future, using model organisms," he continued. With the targeted switching on and off of these genes using different experimental methods, comparative statements about the mode of action of the enzyme and the physiological consequences for the organism will be possible.

What makes the Red Queen tick?

Jan 23, 2019

Kiel Evolution Center provides new insights into the genetic basis of evolutionary dynamics

"Now, here, you see, it takes all the running you can do, to keep in the same place" This advice from the Red Queen in the book "Through the Looking-Glass" by the British author Lewis Carroll serves as a metaphor for a fundamental principle in the field of evolutionary biology. The "Red Queen hypothesis", named after Carroll’s figure, states that all living organisms must constantly adapt and change, in order to survive in a constantly-changing environment. This pressure to change determines the resulting evolutionary dynamics, i.e. the ongoing reciprocal adaptations of various organisms to each other and to altered environmental conditions. Although the “Red Queen hypothesis” has been explored comprehensively at the theoretical level, to date a detailed understanding of the underlying selection mechanisms and the genes involved is still missing. A research team from the Kiel Evolution Center (KEC) at Kiel University (CAU) and the Max-Planck Institute for Evolutionary Biology (MPI) together with international colleagues, has now presented an experimental analysis of these dynamics, and the genetic information which controls this process. The researchers published their results in the current issue of the journal Proceedings of the National Academy of Sciences (PNAS).

In order to experimentally investigate the underlying evolutionary processes, the Kiel researchers focused on the coevolution of the nematode (or thread worm) Caenorhabditis elegans and its bacterial pathogen Bacillus thuringiensis. The study revealed that different factors shape coevolution in the host and pathogen: in the host, the evolutionary response is driven by changes in different genome regions at different time points. In contrast, in the pathogen, adaptation is determined by frequency changes of certain mobile genetic elements, in this case certain so-called plasmids. "The genetic processes underlying rapid host-pathogen coevolution are more complicated than previously assumed, and differ significantly in host and pathogen," said Professor Hinrich Schulenburg, head of the Evolutionary Ecology and Genetics research group at the CAU, KEC spokesperson, and also fellow at the MPI. “The Red Queen thus works differently than we thought, and in particular the role of plasmids and their frequency have not been sufficiently taken into account thus far," continued Schulenburg.

These two processes of rapid evolutionary adaptation can be illustrated using the analogy of a football game: the respective genetic make-up of the host organism and pathogen may be compared with two teams, which must adapt to compete against each other. For example, if one team has a particularly strong attack, then the other team can respond by strengthening its own defence and simply sending a larger number of defense players onto the field. In a figurative sense, this is the approach used by the pathogen, which increases the number of mobile elements, and thus improves its ability to adapt. The nematode, on the other hand, figuratively speaking, exchanges its entire team. Specifically, this means that it adapts to the pathogen though changes in different genome regions at different time points.

In order to study the reciprocal adaptation of worm and bacteria in evolution experiments, the researchers repeatedly infected populations of nematodes with a specific strain of the pathogen. The research team monitored the ensuing coevolutionary changes in the two organisms, characterizing both phenotypic as well as genetic modifications. In this context, a particularly useful characteristic of the nematode Caenorhabiditis elegans is that it survives freezing, allowing direct comparison of offspring with their ancestors - great-grandchildren and great-grandparents can thus be set in direct relationship with each other. The scientists took advantage of this particular characteristic in order to compare worms at different stages of adaptation to the pathogen. In doing so, they discovered that coevolution occurs extremely fast, within a few generations. Likewise, it also became clear that the selection pressure on the pathogens led to changes in the frequency of specific plasmids; these are responsible for the production of toxins which are harmful to the host.

The Kiel researchers believe that the results of their experiments may have uncovered a universal principle underlying rapid evolution of pathogens. Such rapid adaptive responses could be facilitated through changes in the frequency of mobile genetic elements. This is likely to apply to other pathogens, too. Diverse pathogens possess plasmids that often carry the genes for so-called virulence factors, i.e. genetic information which determines the harmfulness for the host organism. "It is possible that pathogens adapt particularly quickly to their hosts, by simply adjusting the frequency of their plasmids, or other mobile elements. New mutations are then not necessary, at least initially," explained Schulenburg. "However, this aspect has not yet been well studied, even though such frequency differences might be important for the assessment of virulence, and thus potentially also for medical diagnosis of infectious disease," concludes Schulenburg.

Cellular memory outwits pathogens

The World Health Organization (WHO) warns that seemingly harmless bacterial infections could develop into one of the leading causes of death in the next few years, particularly in the industrialised countries. This dramatic threat arose because, in many cases, the antibiotics that have been prescribed for decades as a standard treatment have become ineffective due to increasing resistance, and this trend continues to gather pace. The root of the problem is the germs’ rapid evolutionary adaptation to the drugs used to combat them. The consequence is that even new antibiotics can become ineffective within a short period of time. Researchers around the world are therefore pursuing an alternative approach to the worsening antibiotics crisis, in order to regain the upper hand. They are trying to prolong the effectiveness of currently available active substances, through the application of evolutionary biological principles. A research team from the Kiel Evolution Center (KEC) at Kiel University (CAU) has teamed up with colleagues at the Max Planck Institute for Evolutionary Biology in Plön and Uppsala University in Sweden to reveal a previously-unknown principle, which enables a completely new and at the same time highly sustainable form of treatment. The scientists published their results yesterday in the renowned scientific journal PNAS.

The treatment process investigated makes use of a simple principle: short-term application of a particular antibiotic is followed by another antibiotic with a different mechanism of action. Using the example of the bacterium Pseudomonas aeruginosa, which according to the WHO is one of the most critical threats of a multidrug resistant bacterium, the Kiel researchers tested the temporal alternation of antibiotics with different mechanisms of action. To do so, they examined around 200 bacterial populations in an evolution experiment over a total of 500 generations, and observed the effects of different antibiotics and various sequential treatment protocols. They discovered that the most effective sequential protocol started with a penicillin-like substance followed by a so-called aminoglycoside, especially if changes happen in short intervals.

"A short initial treatment makes the germs vulnerable, because it enables easier penetration of the bacterial cells by another drug. The second antibiotic basically finishes the job, and properly kills the remaining bacteria," explained Professor Hinrich Schulenburg, head of the Evolutionary Ecology and Genetics research group at the CAU, and KEC spokesperson. This effect is entirely dependent on the sequence of the alternating antibiotics. The sensitizing drug must be applied first, since it apparently modifies the structure of the bacterial cell walls, and thereby opens the door for the second antibiotic. In addition, the speed and the pattern of the sequence are decisive: "If we alternate the two drugs faster than in normal antibiotic treatment, and at random intervals, the then resistance evolution is inhibited most effectively," continued Schulenburg.

The reason for the success of the sequential treatment is the so-called cellular memory of the bacterial pathogens. The first antibiotic changes the cellular properties of the germs over multiple generations, to such an extent that the second antibiotic functions even better - despite being administered later. "It’s almost like the first antibiotic opens a door, which provides easier entry for the second antibiotic," explained Dr Roderich Römhild, research associate in the Evolutionary Ecology and Genetics research group, and first author of the publication. "This approach is particularly promising from an evolutionary point of view, since the pathogens are now forced to evolve a defence against opening the door - and thus against the cellular memory effect - instead of direct resistance to the antibiotic," said Römhild. In the experiment, a significant reduction in resistance was indeed confirmed.

Most surprisingly, around 30 years ago, exactly the same treatment protocol as the one proposed now was by coincidence tested on patients - with impressive results: in almost all cases, pathogen abundance was significantly reduced following the sequential antibiotic treatment; in half of the cases, the pathogens could no longer be detected, and the sequential protocol was clearly more effective than the standard treatment. However, the method never became part of medical practice, most likely because of the lack of an explanation for treatment success. "We are convinced that with our new results on the cellular memory effect, we have now found the missing explanation," emphasised Schulenburg. "The new work provides yet another example of how, with the help of evolutionary concepts and methods, we can obtain new ideas for sustainable treatment approaches," summarised the KEC spokesperson.

Evolution of Metabolic Dependency as Base for Ancestral Symbiosis

Jun 26, 2018

Kiel research team describes the fundamental mechanisms which control the evolutionary ancient symbiotic relationship between algae and cnidarians for the first time

When life on earth developed, symbiotic associations arose as a successful strategy millions of years ago, with which organisms of different species cooperate as a close-knit community, to gain an advantage in the struggle for survival. However, we still largely do not know why they do this, what the real benefits of such partnerships are, and which molecular mechanisms are important. Scientists from the Collaborative Research Centre (CRC) 1182 “Origin and Function of Metaorganisms” at Kiel University (CAU), together with Japanese researchers from the Okinawa Institute of Science and Technology (OIST) and Okayama University, have now presented the first comprehensive characterisation of symbiotic interactions, using the example of the cooperation between the freshwater polyp Hydra and the Chlorella algae living inside its cells. Their results have been jointly published in the current issue of the internationally-renowned scientific journal eLife.

In order to investigate the fundamental mechanisms of this symbiosis, the research team focused on the metabolic relationships between Hydra and its algae symbiont. The organisms live in a so-called photosynthetic symbiosis: the algae provide their host with certain metabolic products which they obtain from the conversion of solar energy. In return, they obtain nutrients from the polyps which they cannot acquire by themselves. “This form of coexistence between cnidarians and algae is an extreme form of symbiosis, in which the algae can no longer survive without their host. The symbiotic algae even give up parts of their own genetic information, and instead use the corresponding structures of the freshwater polyps,” explained Professor Thomas Bosch, cell and developmental biologist at the CAU and spokesperson for the CRC 1182, regarding the extent of the co-dependence between the species. The Hydra are also highly dependent on their symbionts, since the Chlorella colonisation boosts their reproductive success, so the organisms’ viability would be at a considerable disadvantage without the algae.

“Our results also show which specific tools are required at a genetic and molecular level to ensure that a durable and stable symbiosis can develop in the course of evolution,” continued Bosch. On the one hand, laboratory studies revealed that the presence of the symbionts led to significant up-regulation of certain Hydra genes responsible for the metabolism, boosting the nutrient transport between host and symbiont. On the other hand, analysis of the genome of the symbiotic algae revealed that the symbiont is missing the genetic components required to utilise nitrogen, so that the nutrient supply must be partly taken over by the host.

Overall, this new publication answers one of the most important research questions in the first funding phase of the CRC 1182: the driving forces behind the evolution and long-term stability of a symbiosis. The analysis of the interactions between Hydra polyps and algae makes it clear that the co-evolution of organisms can be driven in particular by the possibility of mutual nutrient exchange. The scientists in Kiel, together with their international colleagues, now plan to build on the results of their research and investigate more complex, multi-organismic interaction networks.

A better understanding of the symbiotic relationships between cnidarians and algae is not only valuable in terms of basic scientific knowledge gained, but can also serve as a model for the assessment of climate change, associated with the change of marine ecosystems: corals, for example, are greatly threatened by the impact of global changes since their ability to absorb nutrients is dramatically affected by changes in the nutrient content of sea water. In turn, the diverse, vibrant, tropical reef-based communities depend on the health and growth of the corals. As corals – like freshwater polyps – are dependent on certain symbiotic bacteria for their nutrient uptake, a more accurate understanding of the underlying mechanisms is required. Further research is necessary to determine whether the new knowledge gained is also applicable to the symbiosis of corals and bacteria, and if this can lead to possible future adaptation strategies for protecting endangered tropical coral reefs.

Cancer diagnosis: no more needles?

May 25, 2018

Kiel University research team proposes extracting genetic material for research and diagnostic purposes from urine in future

Urine is an everyday liquid which most people pay little attention to and regard as rather unpleasant. It’s quite the opposite for a group of clinical researchers from Kiel University, the University Medical Center Schleswig-Holstein (UKSH) and the Lithuanian University of Health Sciences in Kaunas, who are convinced of the diagnostic potential of this yellowish liquid. The reason for this is the genetic material that urine contains – especially the so-called cell-free DNA - which offers new opportunities for cancer diagnostics. The researchers in the lab were able to extract just as much as cell-free DNA from 60 ml of urine (about half a urine beaker) as from a 10 ml blood sample. The research team is working on developing new procedures to extract cell-free DNA from urine for this purpose. Together with their international colleagues, the researchers from the Institute of Clinical Molecular Biology (IKMB) at Kiel University have now published their findings today in the current issue of the journal BioTechniques.

The term cell-free DNA refers to fragments of genetic information that are found outside of cells in various bodily fluids. These DNA components originate when body cells die - but also when tumour cells die. They are initially released into the bloodstream, and from there also make their way into the urine. The research team initially encountered a series of problems: the amount of DNA in urine differs greatly from person to person, and even varies significantly in the same person from day to day. This meant that the DNA concentrations in the samples were initially sometimes too low, so that the researchers had to increase the respective quantities of urine collected. They also regularly observed that the urine of healthy women contains more than twice as much cell-free DNA than the identical amount of urine in healthy men. This factor must be taken into account in future cancer diagnostics, so that these gender-specific differences do not distort the results.

To date, tests for diagnosing cancer are mostly based on blood samples. Some of these blood tests use cell-free DNA, which may originate from a possible tumour, to identify certain types of lung and colon cancer. In the next twelve months, the scientists plan to carry out further research in the IKMB laboratory at Kiel University, to determine whether genetic material from urine is as suitable for clinical research and diagnostics as blood. "To do so, we will examine available samples from study participants at the University Medical Centre, and compare the genetic traces of a tumour in the blood plasma and urine to determine whether both methods can reliably detect the disease," said Michael Forster, a scientist at the Institute of Clinical Molecular Biology at Kiel University.

In future, the researchers in Kiel hope to develop a urine-based test which is as reliable as traditional blood tests. This would primarily benefit patients, who would be spared the unpleasant blood withdrawal. In addition, such a test procedure would be faster and less expensive than the previous methods - for example, unlike with blood tests, no medical personnel are required when taking urine samples. "In the United States, a similar test procedure is already commercially available for cancer research. Recently, an international research team also presented a new urine test, which has not yet been clinically approved, for certain tumours in the urinary tract," said Forster regarding the current state of progress. "The introduction of new urine-based clinical tests in Germany still requires several years of clinical research, as well as further cost/benefit analysis," continued the molecular geneticist.

The follow-up research will be carried out in cooperation with external clinical research groups, within the framework of the new Competence Centre for Genome Analysis Kiel (CCGA Kiel). The CCGA Kiel is Germany's largest academic high-throughput sequencing centre. It has received funding from the German Research Foundation (DFG) and the Federal Ministry of Education and Research (BMBF). Operating one of the four newly-created sequencing super-centres in Germany, Kiel University is servicing the exploding demand for complex genome analysis in the life sciences,.

www.uni-kiel.de/download/pm/2018/2018-165-1.jpg
The leader of the study, Michael Forster, together with his colleagues Regina Fredrik (left) and Nicole Braun from the Institute of Clinical Molecular Biology at Kiel University.
Photo: Christian Urban, Kiel University

What the metabolism reveals about the origin of life

May 07, 2018

Kiel botanist proposes new theory for the simultaneous evolution of opposing metabolic processes

Which came first, the chicken or the egg? This classical ‘chicken-or-egg’ dilemma applies in particular to the developmental processes of life on earth. The basis of evolution was a gradual transition from purely chemical reactions towards the ability of the first life forms to convert carbon via metabolic processes, with the help of enzymes. In this transition, early life forms soon developed different strategies for energy production and matter conversion.

In principle, science distinguishes between so-called heterotrophic and autotrophic organisms: the first group, which includes all animals for example, uses various organic substances as energy sources. Their metabolic processes produce CO2 - amongst other things - during respiration. In contrast, autotrophic organisms exclusively use inorganic carbon compounds for their metabolism. This group includes all plants, which carry out photosynthesis and thereby bind CO2 to gain energy from sunlight.

In evolution research, scientists around the world have long discussed which of the two basic metabolic strategies developed first - autotrophy or heterotrophy, i.e. photosynthesis or respiration. Dr Kirstin Gutekunst, research associate in the Plant Cell Physiology and Biotechnology Group at the Botanical Institute at Kiel University, proposes instead that both developments may have occurred simultaneously and in parallel. The Kiel botanist presents this novel theory for discussion, which she has titled "Hypothesis on the Synchronistic Evolution of Autotrophy and Heterotrophy", in the journal Trends in Biochemical Sciences.

Gutekunst argues as follows: in terms of matter conversion, the earth represents a closed system. The quantity of every kind of matter on earth cannot be changed - it is only continuously converted and reassembled. There must therefore be a balance in such a system - otherwise certain substances would be permanently removed and others permanently added. The logical conclusion is that for every metabolic process, there must be a corresponding opposing process - either within the same organism, or in two different organisms which have opposing metabolic processes. A third core argument of the new hypothesis lies in the fact that the main drivers of the metabolism, the enzymes, can inherently act in two directions - so therefore, every metabolic reaction can be reversed by the corresponding opposing reaction. Metabolic processes overall are not linear, but rather cyclical, and have a global balance of materials.

"The current scientific knowledge suggests that heterotrophy and autotrophy cannot have developed independently of each other. In a closed system that is characterised by a balance of materials, then both metabolic processes are interdependent," said Kirstin Gutekunst. "Just like neither the chicken nor the egg could have originated first, so too heterotrophic and autotrophic organisms cannot have developed after each other," continued the Kiel plant researcher. An example of this kind of balance of materials can be found in cyanobacteria, also known as blue-green algae. They combine the metabolic processes of photosynthesis and respiration in one organism, and thus display heterotrophic and autotrophic properties at the same time. Here, these processes are particularly closely linked, and are based on identical molecular components.

The new theory of the Kiel researcher could thus provide impetus to re-evaluating the existing conception of the origin of life on earth in future. In principle, the question of origin can only be viewed hypothetically. However, Gutekunst’s theory offers credible indices against the idea of a singular origin, which in essence is technically based on an unscientific idea of creation. In contrast, the proposed synchronistic hypothesis suggests a duality right from the beginning of evolution. If metabolic processes based on the effect of enzymes are acknowledged as a characteristic of life, then for each reaction there must also be an opposing reaction. Such an evolution can therefore only have started at the same time, and from there onwards developed in parallel. Gutekunst’s thesis is thus a strong argument against the assumption of a singular origin of autotrophy or heterotrophy.

The publication forms part of the plant research conducted within the priority research area "Kiel Life Science" at Kiel University. Currently, the scientists in this area are striving to network with each other better, and to encourage mutual exchange of ideas and information. In this context, together with partner institutions in the region, they are preparing the formation of an independent, interdisciplinary centre for plant research at Kiel University.

Original publication:
Kirstin Gutekunst (2018): Hypothesis on the Synchronistic Evolution of Autotrophy and Heterotrophy Trends in Biochemical Sciencesdoi.org/10.1016/j.tibs.2018.03.008

Photos are available to download:www.uni-kiel.de/download/pm/2018/2018-134-1.jpg
Caption: The Hypothesis on the Synchronistic Evolution of Autotrophy and Heterotrophy assumes that the opposing processes must have developed at the same time.
Image: Dr Kirstin Gutekunst

Conquering the Extreme

How microorganisms support multicellular organisms with the colonisation of hostile environments

From hot and nutrient-poor deserts to alternating dry and wet intertidal zones, right through to the highest water pressure and permanent darkness in the deep sea: in the course of its development over millions of years, life has conquered even the most extreme places on earth. That termites can live off indigestible wood, plants can exist in deserts - seemingly without water and nutrients, or sea anemones can tolerate the constant change between underwater and dry environments in intertidal zones, apparently also depends on close cooperation with their bacterial symbionts. Life scientists around the world are currently investigating the manner in which the symbiotic interaction of microorganisms and hosts, in the functional unit of a metaorganism, supports the colonisation of such extreme habitats. An international research team under the leadership of the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms” at Kiel University has now presented an inventory of mechanisms, with which the interactions of hosts and symbionts support life under extreme environmental conditions, or even make it possible at all. Together with colleagues from Saudi Arabia’s King Abdullah University of Science and Technology (KAUST), the researchers have now described in detail for the first time in the scientific journal Zoology how microorganisms can promote the growth and the evolutionary fitness of different organisms in extreme locations.

An important factor in response to changing living conditions is time. If the environment at a particular place changes very quickly, for example through drastic change in physical and chemical conditions such as light or oxygen levels, the more highly-developed multicellular organisms in particular find the adjustment difficult. Their ability to adapt is too slow, because the required genetic change can only be completed over the course of several generations. "Here microorganisms can give their host organisms an advantage," emphasised Professor Thomas Bosch, cell and developmental biologist at Kiel University and spokesperson for the CRC 1182. "With bacteria, for example, the evolutionary processes occur much more rapidly. They can partially transfer this ability to respond much faster to environmental changes to their hosts, and thereby assist the hosts with adaptation," continued Bosch.

The lack of food or the inability to actually use the available nutrients further limits the available habitats. The metabolisms of many organisms are geared to specific optimal living conditions, and struggle to cope in extreme areas. Here too, it is often the symbiotic relationships with bacteria which enable plants and animals to expand the functioning of their own metabolisms. Thus, different organisms can, for example, exchange nutrients with their bacterial partners, and thereby utilise food sources which their metabolisms otherwise could not process.

Certain symbiotic bacteria, which colonise the roots of plants, help them to absorb elements such as nitrogen and other minerals in dry and nutrient-poor locations. Other bacteria support plant growth by increasing tolerance to saline soil. In the future, researchers will focus on investigating such helpful bacterial cultures, regarding their applicability to crops. Potentially, a better understanding of plants as metaorganisms could also help to utilise previously-unusable deserts for agriculture in the future.

In addition, microbial symbionts enable various organisms to develop a high tolerance towards a rapidly-changing environment: fixed cnidarians in the inter-tidal zones of different oceans can, for example, quickly adapt to the extreme changes in their living conditions because they can also abruptly change the composition of their bacterial colonisation. Behind this lie mechanisms such as the direct exchange of genetic information between different bacterial species, which controls the exclusion or inclusion of specific types of bacteria in the metaorganism. "In sea anemones, their bacterial colonisation changes in accordance with the prevailing site conditions," emphasised Dr Sebastian Fraune, research associate at the Zoological Institute at Kiel University. "The organisms can potentially save this flexible bacterial configuration, and recall it in the event of a change in their habitat, in order to cope with the new conditions," continued Fraune.

From the investigation of this bacterial-controlled ability to adapt to fast-changing environmental conditions, it may be possible in future to draw conclusions about the effects of climate change on organisms and ecosystems, or even to deduce adaptation strategies. Further research will clarify how the health and fitness of a metaorganism depend on the adaptability of its individual partners, and what effects arise from changing individual elements of this complex structure. The new findings thus emphasise the fundamental importance of researching the multi-organismic relationships between hosts and microorganisms, in particular, too, for the understanding of life in a variable and extreme environment.

A photo is available for download under:www.uni-kiel.de/download/pm/2018/2018-131-1.jpg
Associated microbiota can promote the host’s vigour and proliferation in extreme environments. Such insights may be informative even when attempting to remotely detect the presence of life in extreme conditions on terrestrial planets. The Photograph shows the spectacular Orion Nebula,
taken by ESO’s VLT Survey Telescope (VST).
Credit: ESO/G. Beccari, License: CC BY 4.0, http://www.eso.org/public/images/eso1723a/

Self or nonself?

Feb 23, 2018

Why the interplay of body and microorganisms demands a redefinition of the individual

The individual is synonymous with the human personality, the smallest unit of social structures, and the central concept of existence. In order for science to define this self - which is fundamental to how we see ourselves as humans - biology has traditionally formulated three explanatory approaches, with which the human individual can be clearly set apart from their biologically active environment: the immune system, the brain and the genome make humans unique and distinguishable from all other living beings. However, in light of the new scientific field of metaorganism research, which focuses on the interaction of the organism with its microbial symbionts, this human understanding of being an individual, clearly definable self faces major challenges. Now, an interdisciplinary team of researchers from biology and anthropology, in the framework of the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms" at Kiel University, has formulated in a joint essay on why the metaorganism concept - by now broadly accepted in life sciences - demands a redefinition of the traditional concepts of the self. The ground-breaking article was published by Tobias Rees, professor of anthropology at McGill University and director at Berggruen Institute in Los Angeles, Professor Thomas Bosch, spokesperson of the Kiel CRC 1182, and Angela Douglas, professor of molecular biology and genetics at Cornell University, on Thursday 22 February in the journal PLOS Biology.

The basis of their thesis is the now-proven scientific fact that the human body is not a self-contained entity. Instead, both the development and the functioning of the human organism depend on dynamic and interactive cooperation between human and bacterial cells - or in other words, a balance in the so-called metaorganism, which comprises human and microorganisms. The proportion of bacterial cells in this system is approximately 50 percent.

This high degree of interpenetration of human and bacterial life is the reason why science must take a new look at many biological processes, in light of these multi-organismic relationships. "From the functioning of the organs, to the process of metabolism, right through to protection against infectious diseases - these new findings force us to re-examine and develop a new understanding of all life processes in our body as cooperation between humans and microorganisms," emphasised the cell and developmental biologist Bosch.

For this reason, the classical biological explanations of the individual self - the immune system, the brain and the genome - must also be re-evaluated. Defining the human self on the basis of the immune system is due, amongst other things, to its function of protecting the body against harmful external influences. Therefore, it must somehow be able to distinguish between self and nonself at the molecular level. The result is a sharp dividing line between human and non-human organism, for example in the detection and prevention of pathogens. However, it is now clear that bacteria form an essential component of the immune system: what was thus traditionally considered as part of the human self is actually largely of bacterial origin, i.e. nonself.

It is similar with the classical interpretation of the brain as the seat of core human traits like personality, self-awareness, or emotions: the bacterial colonisation of the body communicates with the nervous system, and then directly or indirectly influences cognitive processes, social behaviour and the psyche. How the brain shapes the human individual is therefore also inextricably linked to the close interconnection between organism and bacteria.

The human genome, i.e. the totality of genetic information, is considered to be unchangeable and unique to every human being. However, it has been determined that microbial genes play a major role in the manifestation of human characteristics. As the bacterial colonisation of the body is not static, the microbial genome also behaves in a highly-variable manner - in contrast with the human one. Its properties can thereby change dramatically over time, and contribute in their variability to the genetic make-up of the body. "Bacteria thus not only influence the human genome, they make up a large part of it," emphasised Rees. The definition of the human individual in terms of a fixed genetic make-up is therefore also outdated, according to Rees.

In a broader context, this revision of the human individual challenges the borders between scientific disciplines. Since the areas of human and non-human can no longer be clearly distinguished, it also calls into question the centuries-old divisions between the arts and the sciences, for example. "The era of metaorganism research is therefore not only associated with an upheaval in the life sciences," stressed Rees. "Rather, metaorganism research is an invitation to the humanities to rethink man after the nature-human separation. And that means learning to rethink human domains such as art or technology and poetry." Metaorganism research also shows how an increasingly-detailed understanding of the genetic and molecular processes of life also redefines science as a whole, added Bosch, who together with Rees is part of the interdisciplinary research programme “Humans and the Microbiome” at the Canadian Institute for Advanced Research (CIFAR).

Photos/material is available for download:www.uni-kiel.de/download/pm/2018/2018-045-1.jpg
Caption: The traditional decoupling of man from nature, such as depicted by Caspar David Friedrich at the beginning of the 19th century, is called into question in the era of the metaorganism: the interactions of body and microorganisms define the human self.

Bacteria as pacemaker for the intestine

Nov 22, 2017

CAU research team discovers connection between microbiome and tissue contractions that are indispensable for healthy bowel functions

Spontaneous contractions of the digestive tract play an important role in almost all animals, and ensure healthy bowel functions. From simple invertebrates to humans, there are consistently similar patterns of movement, through which rhythmic contractions of the muscles facilitate the transport and mixing of the bowel contents. These contractions, known as peristalsis, are essential for the digestive process. With various diseases of the digestive tract, such as severe inflammatory bowel diseases in humans, there are disruptions to the normal peristalsis. To date, very little research has explored the factors underlying the control of these contractions. Now, for the first time, a research team from the Cell and Developmental Biology (Bosch AG) working group at the Zoological Institute at Kiel University (CAU) has been able to prove that the bacterial colonisation of the intestine plays an important role in controlling peristaltic functions. The scientists published their results yesterday - derived from the example of freshwater polyps - in the latest issue of Scientific Reports.

The triggers for the normal spontaneous contractions of the muscle tissue are so-called pacemaker cells of the nervous system. In a specific rhythm and without any external stimulation, they emit electrical impulses, that ultimately reach the smooth muscles of the intestinal wall, and cause them to contract. Although the impulses as such occur by themselves, their frequency and intensity, however, are subject to external influences. "The example of the simple freshwater polyp Hydra has shown us that the bacterial colonisation of the organism can affect the contractions of its digestive cavity. Most likely they do so by modulating the underlying pacemaker signals," said Professor Thomas Bosch, head of the study and spokesperson for the Collaborative Research Centre (CRC) 1182 "Origin and Function of Metaorganisms". Unlike other more complex organisms, Hydra have no bowel in the true sense of the word. Their simple body cavity assumes, amongst other things, the function of a digestive tract; the surrounding tissue also exhibits the typical contractions associated with more highly-developed intestines.

To find out how peristalsis is regulated in the freshwater polyps, the researchers compared normal Hydra which had typical bacterial colonisation with those that had their microbiome completely removed with an antibiotic cocktail. In comparison, these organisms without bacterial colonisation - also referred to as germ-free polyps - exhibited a reduction in contractions by about half. At the same time, the rhythm of the movements became disrupted, and some of the breaks between the contractions were much longer. Thus, the absence of the typical microbiome in Hydra compromised the peristaltic movements in the body cavity.

In a further step, the scientists restored the specific bacterial colonisation in the germ-free organisms. Initially, they introduced each of the five most common bacterial species found in the Hydra microbiome individually back into the sterile polyps. It turned out that this individual bacterial colonisation has no appreciable effect on the frequency and timing of contractions. Only the joint re-introduction of the five main representatives of the microbiome led to a marked improvement in peristalsis, although even then, the pattern of contractions was not fully normalised. Interestingly, an extract produced from the colonising bacteria had a similarly positive influence.

From these observation the Kiel research team concluded that only the natural Hydra microbiome - characterised by a balance between the bacterial species present - can play an important pacemaker role in peristalsis. They discovered that, in this case, certain molecules secreted by the bacteria can intervene in the control mechanism of the pacemaker cells. As such, bacterial signals can have a decisive effect on the pattern of spontaneous peristaltic contractions. "We were able to demonstrate for the first time that in our simple model organism, the microbiome has an indispensable function in the frequency and timing of tissue contractions," emphasised Bosch.

In addition, the example of the evolutionarily ancient model organism Hydra shows us that the control of vital processes of multicellular organisms by their bacterial symbionts already originated very early in the evolution of life, continued Bosch. These ground-breaking results are especially promising for medical research: "The fundamental explanation of the cooperation between organism and microbiome in regulating peristalsis will in future help us to understand the emergence of severe diseases, which arise from disrupted movement of the intestine," summarised Bosch.

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Caption: The typical contraction pattern of the freshwater polyp Hydra: Contraction and relaxation of the same animal over the course of three minutes.
Animation: Andrea Murillo-Rincon, Dr. Alexander Klimovich

New approach to antibiotic therapy is a dead end for pathogens

The World Health Organization WHO is currently warning of an antibiotics crisis. The fear is that we are moving into a post-antibiotic era, during which simple bacterial infections would no longer be treatable. According to WHO forecasts, antibiotic-resistant pathogens could become the most frequent cause of unnatural deaths within just a few years. This dramatic threat to public health is due to the rapid evolution of resistance to antibiotics, which continues to reduce the spectrum of effective antibacterial drugs. We urgently need new treatments. In addition to developing new antibiotic drugs, a key strategy is to boost the effectiveness of existing antibiotics by new therapeutic approaches.

The Evolutionary Ecology and Genetics research group at Kiel University uses knowledge gained from evolutionary medicine to develop more efficient treatment approaches. As part of the newly-founded Kiel Evolution Center (KEC) at Kiel University, researchers under the direction of Professor Hinrich Schulenburg are investigating how alternative antibiotic treatments affect the evolutionary adaptation of pathogens. In the joint study with international colleagues now published in the scientific journal Molecular Biology and Evolution, they were able to show that in the case of the pathogen Pseudomonas aeruginosa, the evolution of resistance to certain antibiotics leads to an increased susceptibility to other drugs. This concept of so-called "collateral sensitivity" opens up new perspectives in the fight against multi-resistant pathogens.

Together with colleagues, Camilo Barbosa, a doctoral student in the Schulenburg lab, examined which antibiotics can lead to such drug sensitivities after resistance evolution. He based his work on evolution experiments with Pseudomonas aeruginosa in the laboratory. This bacterium is often multi-resistant and particularly dangerous for immunocompromised patients. In the experiment, the pathogen was exposed to ever-higher doses of eight different antibiotics, in 12-hour intervals. As a consequence, the bacterium evolved resistance to each of the drugs. In the next step, the researchers tested how the resistant pathogens responded to other antibiotics which they had not yet come into contact with. In this way, they were able to determine which resistances simultaneously resulted in a sensitivity to another drug.

The combination of antibiotics with different mechanisms of action was particularly effective - especially if aminoglycosides and penicillins were included. The study of the genetic basis of the evolved resistances showed that three specific genes of the bacterium can make them both resistant and vulnerable at the same time. "The combined or alternating application of antibiotics with reciprocal sensitivities could help to drive pathogens into an evolutionary dead end: as soon as they become resistant to one drug, they are sensitive to the other, and vice versa," said Schulenburg, to emphasize the importance of the work. Even though the results are based on laboratory experiments, there is thus hope: a targeted combination of the currently-effective antibiotics could at least give us a break in the fight against multi-resistant pathogens, continued Schulenburg.

Switching mutations on and off again

Apr 12, 2016

Kiel research team facilitates functional genomics with new procedure

Mould is primarily associated with various health risks. However, it
also plays a lesser-known role, but one which is particularly important
in biotechnology. The mould (ascomycete) Aspergillus niger, for
example, has been used for for around 100 years to industrially produce
citric acid, which is used as a preservative additive in many
foodstuffs. In order to research the genetic mechanisms which could shed
light on the potential application spectrum of mould and its metabolic
products, a research team from Kiel University has developed a new
procedure in collaboration with colleagues from Leiden University in the
Netherlands. Read more...

Why the Japanese live longer

Nov 13, 2015

Kiel-based research team shows positive influence on life span of bioactive plant compounds in green tea and soy

A research team at the Institute of Human Nutrition and Food Science at
Kiel University has discovered promising links between life expectancy
and two phytochemicals - the so-called catechins and isoflavones. The
underlying research by the Kiel-based scientists recently appeared in
the two journals Oncotarget and The FASEB Journal. Read more...

Marine fungi contain promising anti-cancer compounds

Oct 28, 2015

A Kiel-based research team has identified fungi genes that can develop anti-cancer compounds

To date, the ocean is one of our planet's least researched habitats.
Researchers suspect that the seas and oceans hold an enormous knowledge
potential and are therefore searching for new substances to treat
diseases here. In the EU "Marine Fungi" project, international
scientists have now systematically looked for such substances
specifically in fungi from the sea, with help from Kiel University and
the GEOMAR Helmholtz Centre for Ocean Research Kiel. Read more...

New strategy for fighting antibiotic-resistant pathogens

Oct 16, 2015

Daily switching of antibiotics inhibits the evolution of resistance

Rapid evolution of resistance to antibiotics represents an increasingly
dramatic risk for public health. In fewer than 20 years from now,
antibiotic-resistant pathogens could become one of the most frequent
causes of unnatural deaths. Medicine is therefore facing the particular
challenge of continuing to ensure the successful treatment of bacterial
infections - despite an ever-shrinking spectrum of effective
antibiotics. Recent research by a group of scientists at Kiel University
has now shown that there are possible ways to prolong the effectiveness
of the antibiotics that are currently available. Read more...

Nematode worms hitch a ride on slugs

Slugs and other invertebrates provide essential public transport for small worms including Caenorhabditis elegans
in the search for food, as researchers from Kiel University have now
found out. These worms are around a millimeter long and commonly found
in short-lived environments, such as decomposing fruit or other rotting
plant material. Read more...

Live from the Evolution Lab

Jun 05, 2015

Study on coevolution between host and pathogens sheds new light on evolutionary dynamics.

Every
year, new cold and flu pathogens occur and problematic pathogens such
as Ebola cause global alarm at regular intervals. The key to a better
understanding of disease epidemics lies in the adaptability and thus in
the evolution of the pathogens that cause disease. With the aid of
innovative experiments in the lab, researchers in the research group
Evolutionary Ecology and Genetics at the Christian Albrecht University
of Kiel (CAU) have now been able to gain important insights into the
evolution of pathogens. Read more...

Hidden safety switch: New findings on death receptors in cancer cells

Jun 10, 2015

Achieving
a better molecular understanding of the role played in the occurrence
of cancer of so-called death receptors which make the progression of
pancreatic cancer in particular especially aggressive and almost always
fatal – this is the goal of scientists at the Institute for Experimental
Tumor Research at the Christian Albrecht University of Kiel (CAU). Read more...